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