Hello, I appreciate if someone can help me figure out why I get this error.
Could not display BAM file, error was:file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Here are the steps so far:
- uploaded and checked the quality of 3 FASTQ sequences (FASTqSanger, paired-end, with ref genome:hg19)
- Mapped using BWA-MEM tool (now I have 3 BAM files)
when I use AddOrReplaceReadGroups it immediately generates this error:
QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT Could not display BAM file, error was: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
I have tried the followings ways of running AddorReplace... tool:
With only one file, that is the output from BWA-MEM which is a BAM file and without any auto-assign. Then it won't let me execute unless I enter a value for Library name(LB) for which I entered Coriell (don't know if this is correct). It also asked for Read Group Identifier(ID) for which I entered 1
With only one file and all auto-signs on, same error.
With all 3 files (batch), same error
Should I modify the output BAM file from BWA-MEM tool to be able to use it with AddorReplace?
Thank you so much, Beeta
(admin: text display reformatted)