Re: [Geuvadis_rna_analysis] GEM .bam-files does not have headers - geuvadis_rna_analysis@lists.crg.es

Thasso Griebel

18 Jun 18 Jun

12:03 p.m.

New subject: [Geuvadis_rna_analysis] GEM .bam-files does not have headers

hey, I am curious, because the GEM-2-SAM converter adds a basic header to the SAM file and this is also included in the BAM. When I do a samtools view -H NA20805-NA20805.4.M_120208.bam I get @HD VN:1.3 @SQ SN:chr1 LN:249250621 @SQ SN:chr10 LN:135534747 @SQ SN:chr11 LN:135006516 @SQ SN:chr12 LN:133851895 @SQ SN:chr13 LN:115169878 @SQ SN:chr14 LN:107349540 @SQ SN:chr15 LN:102531392 @SQ SN:chr16 LN:90354753 @SQ SN:chr17 LN:81195210 @SQ SN:chr18 LN:78077248 @SQ SN:chr19 LN:59128983 @SQ SN:chr2 LN:243199373 @SQ SN:chr20 LN:63025520 @SQ SN:chr21 LN:48129895 @SQ SN:chr22 LN:51304566 @SQ SN:chr3 LN:198022430 @SQ SN:chr4 LN:191154276 @SQ SN:chr5 LN:180915260 @SQ SN:chr6 LN:171115067 @SQ SN:chr7 LN:159138663 @SQ SN:chr8 LN:146364022 @SQ SN:chr9 LN:141213431 @SQ SN:chrX LN:155270560 @SQ SN:chrY LN:59373566 @RG ID:0 PG:GEM PL:ILLUMINA SM:0 @PG ID:GEM PN:gem-2-sam VN:1.306 so basic chromosome information is contained. Is there a problem with this part of the header or is there other information missing ? best, -Thasso 2012/6/18 Tuuli Lappalainen <Tuuli.Lappalainen(a)unige.ch>

...

Hello, Jonas pointed out that the GEM bam files don't have header lines, which may be a problem in some cases. I uploaded a reference index file (/upload/geuvadis/wp4_rnaseq/main_project/external_data/reference/hg19_AXYM.fa.fai) that can be used at least in samtools as additional information so that header info is not required, or you can also use that to add headers to your bams if you like. best regards, Tuuli Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch On 6/18/12 11:29 AM, Jonas Carlsson wrote:

Hello! When I tried to run QC-analysis on the GEM-files many of the analysis modules failed because there is no header in the .bam-files. Is this a mistake or by choice? /Jonas

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-- Thasso Griebel, Functional Bioinformatics Parc Cientific Barcelona (PCB), 08028 Barcelona dept Centre Nacional d'Anàlisi Genòmica (CNAG) c/Baldiri Reixac 4-6, Torre I, 2nd floor

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Jonas Carlsson

1:13 p.m.

New subject: [Geuvadis_rna_analysis] GEM .bam-files does not have headers

Hello! You are right, the header is there (I forgot the -H) but that does not explain why the QC-program complains that there is no header. Well, well, I guess that is my problem. /Jonas On 06/18/2012 12:03 PM, Thasso Griebel wrote:

...

hey, I am curious, because the GEM-2-SAM converter adds a basic header to the SAM file and this is also included in the BAM. When I do a samtools view -H NA20805-NA20805.4.M_120208.bam I get @HD VN:1.3 @SQ SN:chr1 LN:249250621 @SQ SN:chr10 LN:135534747 @SQ SN:chr11 LN:135006516 @SQ SN:chr12 LN:133851895 @SQ SN:chr13 LN:115169878 @SQ SN:chr14 LN:107349540 @SQ SN:chr15 LN:102531392 @SQ SN:chr16 LN:90354753 @SQ SN:chr17 LN:81195210 @SQ SN:chr18 LN:78077248 @SQ SN:chr19 LN:59128983 @SQ SN:chr2 LN:243199373 @SQ SN:chr20 LN:63025520 @SQ SN:chr21 LN:48129895 @SQ SN:chr22 LN:51304566 @SQ SN:chr3 LN:198022430 @SQ SN:chr4 LN:191154276 @SQ SN:chr5 LN:180915260 @SQ SN:chr6 LN:171115067 @SQ SN:chr7 LN:159138663 @SQ SN:chr8 LN:146364022 @SQ SN:chr9 LN:141213431 @SQ SN:chrX LN:155270560 @SQ SN:chrY LN:59373566 @RG ID:0 PG:GEM PL:ILLUMINA SM:0 @PG ID:GEM PN:gem-2-sam VN:1.306 so basic chromosome information is contained. Is there a problem with this part of the header or is there other information missing ? best, -Thasso 2012/6/18 Tuuli Lappalainen <Tuuli.Lappalainen(a)unige.ch <mailto:Tuuli.Lappalainen@unige.ch>> Hello, Jonas pointed out that the GEM bam files don't have header lines, which may be a problem in some cases. I uploaded a reference index file (/upload/geuvadis/wp4_rnaseq/main_project/external_data/reference/hg19_AXYM.fa.fai) that can be used at least in samtools as additional information so that header info is not required, or you can also use that to add headers to your bams if you like. best regards, Tuuli Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 <tel:%2B41-%280%2922-3795550> tuuli.lappalainen(a)unige.ch <mailto:tuuli.lappalainen@unige.ch> On 6/18/12 11:29 AM, Jonas Carlsson wrote:

Hello! When I tried to run QC-analysis on the GEM-files many of the

analysis

modules failed because there is no header in the .bam-files. Is

this a

mistake or by choice? /Jonas

_______________________________________________ Geuvadis_rna_analysis mailing list Geuvadis_rna_analysis(a)lists.crg.es <mailto:Geuvadis_rna_analysis@lists.crg.es> http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis -- Thasso Griebel, Functional Bioinformatics Parc Cientific Barcelona (PCB), 08028 Barcelona dept Centre Nacional d'Anàlisi Genòmica (CNAG) c/Baldiri Reixac 4-6, Torre I, 2nd floor

Reply

Matthias Barann

3:04 p.m.

New subject: [Geuvadis_rna_analysis] GEM .bam-files does not have headers

Hello, just to let everyone know, the error message I encountered while reading the header was caused by an older version of samtools. It does not give any error with the newest samtools version. I came across this little thread, which suggests that there was a problem with bgzf and the detection of the EOF character in uncompressed BAM files. http://sourceforge.net/mailarchive/message.php?msg_id=27395152 best wishes, Matthias On 18.06.2012 13:32, Matthias Barann wrote:

...

Hey, actually I noticed something similar. Samtools complained about an invalid argument for the EOF check when I indexed a GEM BAM file. Maybe this is the reason for your error, as the eof seems to be checked while reading the header. I wonder if this might be caused by the way GEM generates the bam files (indexing was successful anyway, at least as far as I can see). Another reason could be broken files due to the FTP transfer, though I verified that the md5sum is the same for the file I downloaded and the file on the FTP server. Here the error message:

[bam_header_read] bgzf_check_EOF: Invalid argument

Matthias On 18.06.2012 13:13, Jonas Carlsson wrote:

Hello! You are right, the header is there (I forgot the -H) but that does not explain why the QC-program complains that there is no header. Well, well, I guess that is my problem. /Jonas On 06/18/2012 12:03 PM, Thasso Griebel wrote:

hey, I am curious, because the GEM-2-SAM converter adds a basic header to the SAM file and this is also included in the BAM. When I do a samtools view -H NA20805-NA20805.4.M_120208.bam I get @HD VN:1.3 @SQ SN:chr1 LN:249250621 @SQ SN:chr10 LN:135534747 @SQ SN:chr11 LN:135006516 @SQ SN:chr12 LN:133851895 @SQ SN:chr13 LN:115169878 @SQ SN:chr14 LN:107349540 @SQ SN:chr15 LN:102531392 @SQ SN:chr16 LN:90354753 @SQ SN:chr17 LN:81195210 @SQ SN:chr18 LN:78077248 @SQ SN:chr19 LN:59128983 @SQ SN:chr2 LN:243199373 @SQ SN:chr20 LN:63025520 @SQ SN:chr21 LN:48129895 @SQ SN:chr22 LN:51304566 @SQ SN:chr3 LN:198022430 @SQ SN:chr4 LN:191154276 @SQ SN:chr5 LN:180915260 @SQ SN:chr6 LN:171115067 @SQ SN:chr7 LN:159138663 @SQ SN:chr8 LN:146364022 @SQ SN:chr9 LN:141213431 @SQ SN:chrX LN:155270560 @SQ SN:chrY LN:59373566 @RG ID:0 PG:GEM PL:ILLUMINA SM:0 @PG ID:GEM PN:gem-2-sam VN:1.306 so basic chromosome information is contained. Is there a problem with this part of the header or is there other information missing ? best, -Thasso 2012/6/18 Tuuli Lappalainen <Tuuli.Lappalainen(a)unige.ch <mailto:Tuuli.Lappalainen@unige.ch>> Hello, Jonas pointed out that the GEM bam files don't have header lines, which may be a problem in some cases. I uploaded a reference index file (/upload/geuvadis/wp4_rnaseq/main_project/external_data/reference/hg19_AXYM.fa.fai) that can be used at least in samtools as additional information so that header info is not required, or you can also use that to add headers to your bams if you like. best regards, Tuuli Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 <tel:%2B41-%280%2922-3795550> tuuli.lappalainen(a)unige.ch <mailto:tuuli.lappalainen@unige.ch> On 6/18/12 11:29 AM, Jonas Carlsson wrote:

Hello! When I tried to run QC-analysis on the GEM-files many of the

analysis

modules failed because there is no header in the .bam-files.

Is this a

mistake or by choice? /Jonas

_______________________________________________ Geuvadis_rna_analysis mailing list Geuvadis_rna_analysis(a)lists.crg.es <mailto:Geuvadis_rna_analysis@lists.crg.es> http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis -- Thasso Griebel, Functional Bioinformatics Parc Cientific Barcelona (PCB), 08028 Barcelona dept Centre Nacional d'Anàlisi Genòmica (CNAG) c/Baldiri Reixac 4-6, Torre I, 2nd floor

_______________________________________________ Geuvadis_rna_analysis mailing list Geuvadis_rna_analysis(a)lists.crg.es http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis

-- Matthias Barann Institute of Clinical Molecular Biology Christian Albrechts University Kiel Schittenhelmstr. 12 D-24105 Kiel, Germany m.barann(a)ikmb.uni-kiel.de +49 - (0)431 - 597 8681 (office) _______________________________________________ Geuvadis_rna_analysis mailing list Geuvadis_rna_analysis(a)lists.crg.es http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis

-- Matthias Barann Institute of Clinical Molecular Biology Christian Albrechts University Kiel Schittenhelmstr. 12 D-24105 Kiel, Germany m.barann(a)ikmb.uni-kiel.de +49 - (0)431 - 597 8681 (office)

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