[galaxy-user] Change format with "edit attributes"
Hello, I'm trying to change the format to the output files from Barcode splitter from FASTA to FASTAQ so I can use them in Bowtie for Illumina. I've read that it can be done through the edit attributes, I go to datatype and select fastaq, save and then go to convert format and press convert but the resulting file is 0 bytes and is not recognized by Bowtie. I´ve also tried to upload by copying the link and selecting fastaq as format but in this case, I got the file shown in the picture and it is not recognized by Bowtie again. What can I do?? I don´t know how to continue because I´m not able to change the format to fastaq! Thank you very much for your help in advance Best, Gema <>___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Change format with "edit attributes"
On Wed, Apr 3, 2013 at 3:40 PM, Gema Sanz Santos wrote: > Hello, > > I'm trying to change the format to the output files from Barcode splitter > from FASTA to FASTAQ so I can use them in Bowtie for Illumina. I've read > that it can be done through the edit attributes, I go to datatype and > select fastaq, save and then go to convert format and press convert but the > resulting file is 0 bytes and is not recognized by Bowtie. > > I´ve also tried to upload by copying the link and selecting fastaq as > format but in this case, I got the file shown in the picture and it is not > recognized by Bowtie again. > > > What can I do?? I don´t know how to continue because I´m not able to > change the format to fastaq! > > Thank you very much for your help in advance > > Best, > Gema > > Hi Gema, There seem to be several factors confusing you here. The screenshot shows FASTA data wrongly labelled as FASTQ. The Galaxy "edit attributes" does NOT actually edit the data. There are separate tools which can convert from one format to another, which gives you a new entry in the history (another green box on the right). You can convert from FASTQ to FASTA, but doing the opposite is not possible without inventing quality scores (e.g. give everything score 30). Does that help? Peter <>___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] FW: Change format with "edit attributes"
Hi Peter, Thank you for your fast answer. I just want to know how can I use output files from Barcode splitter to use them into Bowtie for Illumina because I can´t see any tool to convert FASTA to FASTAQ. How can I continue with the mapping using the files from Barcode splitter? Best, Gema From: Peter Cock Date: Wednesday, April 3, 2013 4:42 PM To: Gema Sanz Santos Cc: Subject: Re: [galaxy-user] Change format with "edit attributes" On Wed, Apr 3, 2013 at 3:40 PM, Gema Sanz Santos wrote: > Hello, > > I'm trying to change the format to the output files from Barcode splitter from > FASTA to FASTAQ so I can use them in Bowtie for Illumina. I've read that it > can be done through the edit attributes, I go to datatype and select fastaq, > save and then go to convert format and press convert but the resulting file is > 0 bytes and is not recognized by Bowtie. > > I´ve also tried to upload by copying the link and selecting fastaq as format > but in this case, I got the file shown in the picture and it is not recognized > by Bowtie again. > > > What can I do?? I don´t know how to continue because I´m not able to change > the format to fastaq! > > Thank you very much for your help in advance > > Best, > Gema > Hi Gema, There seem to be several factors confusing you here. The screenshot shows FASTA data wrongly labelled as FASTQ. The Galaxy "edit attributes" does NOT actually edit the data. There are separate tools which can convert from one format to another, which gives you a new entry in the history (another green box on the right). You can convert from FASTQ to FASTA, but doing the opposite is not possible without inventing quality scores (e.g. give everything score 30). Does that help? Peter <>___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Change format with "edit attributes"
Hi Gema, For example, see the "Combine FASTA and QUAL into FASTQ" tool for creating a FASTQ file from FASTA data; when quality data is not provided, fake score values will be used. Thanks for using Galaxy, Dan On Apr 3, 2013, at 10:42 AM, Peter Cock wrote: > > > On Wed, Apr 3, 2013 at 3:40 PM, Gema Sanz Santos wrote: > Hello, > > I'm trying to change the format to the output files from Barcode splitter > from FASTA to FASTAQ so I can use them in Bowtie for Illumina. I've read that > it can be done through the edit attributes, I go to datatype and select > fastaq, save and then go to convert format and press convert but the > resulting file is 0 bytes and is not recognized by Bowtie. > > I´ve also tried to upload by copying the link and selecting fastaq as format > but in this case, I got the file shown in the picture and it is not > recognized by Bowtie again. > > > > What can I do?? I don´t know how to continue because I´m not able to change > the format to fastaq! > > Thank you very much for your help in advance > > Best, > Gema > > > Hi Gema, > > There seem to be several factors confusing you here. > > The screenshot shows FASTA data wrongly labelled as FASTQ. > > The Galaxy "edit attributes" does NOT actually edit the data. There are > separate tools which can convert from one format to another, which gives you > a new entry in the history (another green box on the right). > > You can convert from FASTQ to FASTA, but doing the opposite is not possible > without inventing quality scores (e.g. give everything score 30). > > Does that help? > > Peter > > ___ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Regarding a cuffdiff output
Dear galaxy users Hello. I have a quick question about Cuffdiff analysis. I have obtained two SRA files and converted them to fastq files which were uploaded to Galaxy via FTP server. My analysis was followed by Fastq groomer, Tophat, Cufflinks, Cuffcompare, and eventually Cuffdiff. (Gene annotation was also downloaded from UCSC table browser in GTF format) I've downloaded gene differential expression testing, one of the output files of Cuffdiff, and viewed it in excel sheet. However, I have only zeros recorded for value_1, value_2, log2, test_stat and only ones recorded for p_value and q_value. Is it likely that I might have obtained wrong gene annotation file and caused this problem? Thank you Yona Kim Department of Genetics Rutgers University - New Brunswick Campus ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Phyloviz and problem viewing nexus and newick files
Dear Galaxy users, I'm trying to view files from phylogenetics analyses in Newick or nexus formats. It seems that Phyloviz doesn't work since the last update of Galaxy. Can you inform me about this problem and the possibility to make Phyloviz working on a local instance? When I try on the main galaxy instance, I have the following error number: GURU MEDITATION: #1a7e2c6048fd4852ae09587cba0a09e8 Thank you very much for your help. Best Regards, Yvan -- - Yvan Le Bras, PhD <°>< e-Biogenouest project http://www.e-biogenouest.org CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, 35042 Rennes Cedex yvan.le_b...@irisa.fr ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Change format with "edit attributes"
Hi Gema, Quick comment. If you do have the QUAL file to begin with, I would recommend doing the combine first, then barcode splitter(which can do fastq too), then bowtie. This way you have the benefits of mapping using the real quality score. --Carlos On Wed, Apr 3, 2013 at 11:07 AM, Daniel Blankenberg wrote: > Hi Gema, > > For example, see the "Combine FASTA and QUAL into FASTQ" tool for creating a > FASTQ file from FASTA data; when quality data is not provided, fake score > values will be used. > > > Thanks for using Galaxy, > > Dan > > On Apr 3, 2013, at 10:42 AM, Peter Cock wrote: > > > > On Wed, Apr 3, 2013 at 3:40 PM, Gema Sanz Santos wrote: >> >> Hello, >> >> I'm trying to change the format to the output files from Barcode splitter >> from FASTA to FASTAQ so I can use them in Bowtie for Illumina. I've read >> that it can be done through the edit attributes, I go to datatype and select >> fastaq, save and then go to convert format and press convert but the >> resulting file is 0 bytes and is not recognized by Bowtie. >> >> I´ve also tried to upload by copying the link and selecting fastaq as >> format but in this case, I got the file shown in the picture and it is not >> recognized by Bowtie again. >> >> >> >> What can I do?? I don´t know how to continue because I´m not able to >> change the format to fastaq! >> >> Thank you very much for your help in advance >> >> Best, >> Gema >> > > Hi Gema, > > There seem to be several factors confusing you here. > > The screenshot shows FASTA data wrongly labelled as FASTQ. > > The Galaxy "edit attributes" does NOT actually edit the data. There are > separate tools which can convert from one format to another, which gives you > a new entry in the history (another green box on the right). > > You can convert from FASTQ to FASTA, but doing the opposite is not possible > without inventing quality scores (e.g. give everything score 30). > > Does that help? > > Peter > > ___ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > > ___ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Phyloviz and problem viewing nexus and newick files
Hi, it appears the nexus file you are trying to visualize does not have any "trees" section, what does the newick format tree look like, and did these work before in Galaxy? If you could share the relevant history that would help. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Wed, Apr 3, 2013 at 12:37 PM, Yvan Le Bras wrote: > Dear Galaxy users, > > I'm trying to view files from phylogenetics analyses in Newick or nexus > formats. It seems that Phyloviz doesn't work since the last update of > Galaxy. Can you inform me about this problem and the possibility to make > Phyloviz working on a local instance? When I try on the main galaxy > instance, I have the following error number: > > GURU MEDITATION: #1a7e2c6048fd4852ae09587cba0a09e8 > > Thank you very much for your help. > > > Best Regards, > > > Yvan > > > -- > - > Yvan Le Bras, PhD > <°>< > e-Biogenouest project > http://www.e-biogenouest.org >CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, 35042 > Rennes Cedex > > yvan.le_b...@irisa.fr > > ___ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Using segments of sequences as a reference genome - Bowtie for Illumina
Dear all, My problem seems like something that should have a very simple solution from my end and due to my lack of knowledge in bioinformatics, I am probably messing up with the workflows. The experiment I run is one where we used Miseq to sequence amplicons of a multiplex PCR. We introduced an inhouse barcodeto our PCR products via an adaptor. Miseq data was demultiplexed for the Illumina barcodes using Miseq reporter on intrument software by our service provider and I am trying to run the rest of the process on Galaxy web port with no command prompt programming. The data for R1 and R2 was imported, and then I used barcode splitter to de-multiplex the amplicons after quality triming. (I did not use FASTQ groomer as Miseq data is supposed to be Sanger FastQ than Illumina). Then the sequence trimmer was used to trim the barcode+adaptor sequences. The results of this were re-uploaded and designated as FASTQ for alignment. Now for the reference genome, as our aplicons are of from different sequences, we have segmented FASTA sequences in one file with different FASTA identifiers. When this file was input as the reference genome and mapping was performed using Bowtie for Illumina, the mapping went on with no errors. I could filter the alignment file using SAM filters too. But I can not do any more downstream visualozations, not even SAM to BAM conversion. I suspect that this may be due to an error in the way that the reference genome was formulated but can not get around to figure it out. I would be extremely grateful if you could help me with this issue. I tihnk if I string together the sequences as one it would work, but converting this back for interpretation becomes an issue then. Thank you, Kind Regards, Veranja Veranja Liyanapathirana Graduate Student (Microbiology)___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
