Hello,
I am working with BAM/SAM files generated by MapSplice on (human) RNA-seq paired-end reads from Illumina HiSeq. I want to convert them into fastq in order to realign them (I don't have access to the raw data).
To do this I am trying to use HTSeq-0.5.4p3 with python2.7 using
for a in HTSeq.bundle_multiple_alignments(samfile):
a[0].read.write_to_fastq_file(myfqfile)
The problem is that these Sam files have incorrect Sam fields and I get the error
ValueError: ("Malformed SAM line: MRNM == '*' although flag bit &0x0008 cleared").
The same error is raised with the picard tool SamToFastq.
I know this is a normal error since the Sam files are incorrect but I wanted to know if someone had a workaround for this problem?
I will eventually work on a script to reformat correctly all the Sam files but if someone has one I would be very happy to have it!
Thanks,
Anne
I am working with BAM/SAM files generated by MapSplice on (human) RNA-seq paired-end reads from Illumina HiSeq. I want to convert them into fastq in order to realign them (I don't have access to the raw data).
To do this I am trying to use HTSeq-0.5.4p3 with python2.7 using
for a in HTSeq.bundle_multiple_alignments(samfile):
a[0].read.write_to_fastq_file(myfqfile)
The problem is that these Sam files have incorrect Sam fields and I get the error
ValueError: ("Malformed SAM line: MRNM == '*' although flag bit &0x0008 cleared").
The same error is raised with the picard tool SamToFastq.
I know this is a normal error since the Sam files are incorrect but I wanted to know if someone had a workaround for this problem?
I will eventually work on a script to reformat correctly all the Sam files but if someone has one I would be very happy to have it!
Thanks,
Anne
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