Hi, guys! I'm a complete noobie in computational staff and just trying to learn thing. I want to convert SAM file to BAM and my SAM file does not have a header.
So, I goggle the problem and found one possible solution with -t options from samtools. I created the reference.fa.fai with
command and then tried to run
However, I'm getting the error message
I've tried to use advices from here http://seqanswers.com/forums/showthread.php?t=9650, but still keep getting the same error message.
Please, help!
So, I goggle the problem and found one possible solution with -t options from samtools. I created the reference.fa.fai with
Code:
samtools faidx reference.fa
Code:
samtools view -Sb sam.file -t reference.fa.fai > bam.file
Code:
[sam_header_read2] 35 sequences loaded. Parse error at line 2: missing colon in auxiliary data /var/spool/sge//node091/job_scripts/1441097: line 10: 19514 Aborted (core dumped) samtools view -Sb $in_file.sam -t /$
Please, help!
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