Re: [galaxy-user] Find out sense and antisense sequences
Thank you so much, Jennifer!
Your method is pretty good for filtering the sequences that have "A"
at the 10th base position.But I'm sure if it have employed 10 bp
complementary criterion? For the antisense, the 5' will be T (in
complementary to A). Besides, my library contains other small RNAs.
That's why I concern output files of sense and antisense must have
10bp complementary.
Another quick question, in you regular expression, what does "+" mean?
Thanks!
Zhiqiang
Quoting "Jennifer Jackson" :
Hi Zhiqiang,
Under the tool group "NGS: QC and manipulation" is a tool named
"Manipulate FASTQ". To filter for sequences containing an "A" at
base position 10 and remove them, use the settings are shown in the
attatched .png. Also listed here:
Click on "Add new Match Reads"
Match Reads by: "Sequence Content"
Sequence Match Type: "Regular Expression", using
^.{9}A.+
Click on "Add new Manipulate Reads"
Manipulate Reads on: "Miscellaneous Actions"
Miscellaneous Manipulation Type: "Remove Read"
This will result in the antisense reads being placed in the output,
minus any antisense that happened to have an A at the 10th base
position, which I am not sure is a concern or not.
To output the sense reads, or rather reads with an A at the 10 base
position, change the regular expression to be:
^.{9}[^A].+
The logic is a bit backwards - you are filtering for what you will
be removing - the opposite will be in the output.
Hopefully this helps! Peter's advice about aligning to the genome
and determining strand/orientation vs known transcripts from the
results is mostly likely your second best choice (and more
complicated). Tools in "Interval Operation" group will be of help if
you go down that path.
Best,
Jen
Galaxy team
On 11/26/12 10:47 AM, Zhiqiang Shu wrote:
Hi, Galaxy users!
I have a question on how to find out sense and antisense sequence.
I've got RNA seq data in the fastq format. The sequences inside are
partially complementary to each other (complementary is 10nt, while
entire is about 30nt). How can I separate these sequences into two
groups: sense and antisense (one thing I know is for the sense
sequence the 10th nucleotide is always "A")?
Thanks a lot!
Best,
Zhiqiang
___
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--
Jennifer Jackson
http://galaxyproject.org
--
Zhiqiang Shu/Deng Lab
Department of Biological Science
Florida State University
319 Stadium Dr.
Tallahassee, FL, USA, 32306-4295
z...@bio.fsu.edu
___
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Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
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Re: [galaxy-user] Find out sense and antisense sequences
Hi Zhiqiang,
The regular expressions I shared are just filters. It strictly either
finds sequences with an A at base position 10 (first expression) or
without an A at base position 10 (second expression). All starting left
-> right along the sequence text (or string). This may or may not be
enough to do what you need. I just wanted to give this as an option in
case it would, or perhaps it is a starting place if you can tune it to
be appropriate. If your data contains more than just these two
populations, or will not split appropriately based on this criteria,
then this method will most likely not be the one you want to use.
The plus "+" sign means "one or more" of the proceeding variable, which
in this case was a dot "." that matches any single character with the
exception of a newline (end of line) character, generally noted by a
dollar sign "$".
Regular expressions can be simple or quite tricky - a short crib is on
the form help for the the tool "Filter and Sort -> Select", or you can
search the web for many more comprehensive guidelines, as there is a
component of artistry to creating these. Experimenting and testing to
see what works is the best advice, when used.
Good luck!
Jen
Galaxy team
On 11/27/12 10:07 AM, Zhiqiang Shu wrote:
Thank you so much, Jennifer!
Your method is pretty good for filtering the sequences that have "A"
at the 10th base position.But I'm sure if it have employed 10 bp
complementary criterion? For the antisense, the 5' will be T (in
complementary to A). Besides, my library contains other small RNAs.
That's why I concern output files of sense and antisense must have
10bp complementary.
Another quick question, in you regular expression, what does "+" mean?
Thanks!
Zhiqiang
Quoting "Jennifer Jackson" :
Hi Zhiqiang,
Under the tool group "NGS: QC and manipulation" is a tool named
"Manipulate FASTQ". To filter for sequences containing an "A" at base
position 10 and remove them, use the settings are shown in the
attatched .png. Also listed here:
Click on "Add new Match Reads"
Match Reads by: "Sequence Content"
Sequence Match Type: "Regular Expression", using
^.{9}A.+
Click on "Add new Manipulate Reads"
Manipulate Reads on: "Miscellaneous Actions"
Miscellaneous Manipulation Type: "Remove Read"
This will result in the antisense reads being placed in the output,
minus any antisense that happened to have an A at the 10th base
position, which I am not sure is a concern or not.
To output the sense reads, or rather reads with an A at the 10 base
position, change the regular expression to be:
^.{9}[^A].+
The logic is a bit backwards - you are filtering for what you will be
removing - the opposite will be in the output.
Hopefully this helps! Peter's advice about aligning to the genome and
determining strand/orientation vs known transcripts from the results
is mostly likely your second best choice (and more complicated).
Tools in "Interval Operation" group will be of help if you go down
that path.
Best,
Jen
Galaxy team
On 11/26/12 10:47 AM, Zhiqiang Shu wrote:
Hi, Galaxy users!
I have a question on how to find out sense and antisense sequence.
I've got RNA seq data in the fastq format. The sequences inside are
partially complementary to each other (complementary is 10nt, while
entire is about 30nt). How can I separate these sequences into two
groups: sense and antisense (one thing I know is for the sense
sequence the 10th nucleotide is always "A")?
Thanks a lot!
Best,
Zhiqiang
___
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/
--
Jennifer Jackson
http://galaxyproject.org
--
Zhiqiang Shu/Deng Lab
Department of Biological Science
Florida State University
319 Stadium Dr.
Tallahassee, FL, USA, 32306-4295
z...@bio.fsu.edu
--
Jennifer Jackson
http://galaxyproject.org
___
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/
[galaxy-user] combining two fastq files
Is there an option in galaxy to combine two fastq files? Thanks kanwar ___ 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/
Re: [galaxy-user] combining two fastq files
On Tue, Nov 27, 2012 at 9:51 PM, shamsher jagat wrote: > Is there an option in galaxy to combine two fastq files? > Thanks > > kanwar Yes, but what do you mean by combine? Interleave? Concatenate? 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/
Re: [galaxy-user] combining two fastq files
Hello Kanwar, If you just need to combine two datasets end to end, the tool "Text Manipulation -> Concatenate datasets tail-to-head" is a good choice. Please let us know if you had something else in mind, Jen Galaxy team On 11/27/12 1:51 PM, shamsher jagat wrote: Is there an option in galaxy to combine two fastq files? Thanks kanwar ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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/
Re: [galaxy-user] combining two fastq files
This is my question, too! In my case, I just want to combine two fastq files into only one, for instance, one file come first and then comes the second. How can I make it? Thanks! Zhiqiang Quoting "Peter Cock" : On Tue, Nov 27, 2012 at 9:51 PM, shamsher jagat wrote: Is there an option in galaxy to combine two fastq files? Thanks kanwar Yes, but what do you mean by combine? Interleave? Concatenate? 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/ -- Zhiqiang Shu/Deng Lab Department of Biological Science Florida State University 319 Stadium Dr. Tallahassee, FL, USA, 32306-4295 z...@bio.fsu.edu ___ 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/
Re: [galaxy-user] combining two fastq files
Hi Zhiqiang, Here are the instructions, in case you didn't see the other post: http://lists.bx.psu.edu/pipermail/galaxy-user/2012-November/005576.html Thanks! Jen Galaxy team On 11/27/12 4:31 PM, Zhiqiang Shu wrote: This is my question, too! In my case, I just want to combine two fastq files into only one, for instance, one file come first and then comes the second. How can I make it? Thanks! Zhiqiang Quoting "Peter Cock" : On Tue, Nov 27, 2012 at 9:51 PM, shamsher jagat wrote: Is there an option in galaxy to combine two fastq files? Thanks kanwar Yes, but what do you mean by combine? Interleave? Concatenate? 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/ -- Zhiqiang Shu/Deng Lab Department of Biological Science Florida State University 319 Stadium Dr. Tallahassee, FL, USA, 32306-4295 z...@bio.fsu.edu ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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/
