18 Jun
2012
18 Jun
'12
1:32 p.m.
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:
--
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)
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:
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http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis 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