You put the -x in the wrong place. No, you can not use "PU=sample_1"
instead of "PU:sample_1". BTW, there were multiple follow-ups to this on
biostars a few days ago (https://www.biostars.org/p/166713/#166730).
Devon
--
Devon Ryan, Ph.D.
Email: [email protected]
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany
<[email protected]>
On Tue, Nov 24, 2015 at 11:38 AM, Yaseen Ladak <[email protected]>
wrote:
> Hello Devon,
>
> The following command is giving me an error. Also can I write --rg
> PU=sample_1 instead of --rg PU:sample_1
>
> Command:
> bowtie2 -x --rg-id sample_1 --rg SM:sample_1 --rg LB:sample_1 --rg
> PL:illumina_hi-seq --rg PU:sample_1 bowtie2_index_hg38 -1
> mrg_sample_1_R1_val_1.fq.gz -2 mrg_sample_1_R2_val_2.fq.gz | samtools view
> -Shb - | samtools sort - test_4
>
> Error:
> Warning: --rg was specified without --rg-id also being specified. @RG line
> is not printed unless --rg-id is specified.
> Warning: Output file 'sample_1' was specified without -S. This will not
> work in future Bowtie 2 versions. Please use -S instead.
> Extra parameter(s) specified: “bowtie2_index_hg38”
> Note that if <mates> files are specified using -1/-2, a <singles> file
> cannot
> also be specified. Please run bowtie separately for mates and singles.
> Error: Encountered internal Bowtie 2 exception (#1)
> Command: /usr/local/bin/../Cellar/bowtie2/2.2.6/bin/bowtie2-align-s
> --wrapper basic-0 -x --rg-id --rg SM:sample_1 --rg LB:sample_1 --rg
> PL:illumina_hi-seq --rg PU:sample_1 -1 /tmp/5308.inpipe1 -2
> /tmp/5308.inpipe2 sample_1 bowtie2_index_hg38
> (ERR): bowtie2-align exited with value 1
>
>
> On 20 November 2015 at 21:14, Devon Ryan <[email protected]> wrote:
>
>> You can add the read group directly in bowtie2:
>>
>> bowtie2 -x bowtie2_index_hg38 --rg-id sample1 --rg SM:sample1 ... |
>> samtools view -Su - | samtools sort - output
>>
>> Picard's BuildBamIndex tool might be able to take input from a pipe (I'm
>> pretty sure this doesn't work with samtools at the moment), in which case:
>>
>> ... | picard SortSam INPUT=/dev/stdin OUTPUT=/dev/stdout | tee output.bam
>> | picard BuildBamIndex INPUT=/dev/stdin OUTPUT=output.bam.bai
>>
>> Or something along those regards. I really can't recommend doing this,
>> though. Getting the index in an additional step is going to be a minuscule
>> time savings.
>>
>> Devon
>>
>>
>> On 11/20/2015 08:21 PM, Yaseen Ladak wrote:
>>
>> Hi All,
>>
>> I need some help I want to pipe the output from samtools to picard
>> readgrous commands but I am failing:
>>
>> *bowtie2 -x bowtie2_index_hg38 -1 R1.fq.gz -2 R2.fq.gz | samtools view
>> -Shb - | samtools sort - output*
>>
>> What I want to achieve is the following is to also add the read groups
>> the output.bam file from above command and also index the output bam file
>> with reads groups. I am failing with the following command and I dont know
>> how to also index the output bam file that has the read group.
>>
>> *bowtie2 -x bowtie2_index_hg38 -1 mrg_sample_1_R1_val_1.fq -2
>> mrg_sample_1_R2_val_2.fq | samtools view -Shb - | samtools sort - - |
>> picard AddOrReplaceReadGroups I= output.bam O=rg_output.bam RGID=sample_1
>> RGLB=sample_1 RGPL=illumina_hi-seq RGPU=sample_1 RGSM=sample_1*
>>
>> Can someone please help me?
>> Thanks,
>> Yaseen
>>
>>
>> ------------------------------------------------------------------------------
>>
>>
>>
>> _______________________________________________
>> Samtools-help mailing
>> [email protected]https://lists.sourceforge.net/lists/listinfo/samtools-help
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>> Give your users amazing mobile app experiences with Intel(R) XDK.
>> Use one codebase in this all-in-one HTML5 development environment.
>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>> OSs.
>> http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
>> _______________________________________________
>> Samtools-help mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/samtools-help
>>
>>
>
------------------------------------------------------------------------------
Go from Idea to Many App Stores Faster with Intel(R) XDK
Give your users amazing mobile app experiences with Intel(R) XDK.
Use one codebase in this all-in-one HTML5 development environment.
Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140
_______________________________________________
Samtools-help mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/samtools-help
