Hi Guys,I am trying to convert some sra files into bam format. At the moment, I am using this command from sratoolkit
sam-dump SRR390728 | samtools view -bS - > SRR390728.bam
but unfortunately I got an error message like this:
sam-dump.2.4.2 err: param invalid while validating file within file system module - content-size read from local file is invalid.
Having said that, I still get a bam file as output at the end. Can I ignore that error msg and continue with peak calling? Also how I can convert multiple sra files to bam in one go? Many thanks!
sam-dump SRR390728.sra > SRR390728.sam
Once you have your SAM file:
module load SAMTools
samtools view -b -S SRR390728.sam > SRR390728.bam
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written
by
gauravsingh.singh86 •
Note that loading samtools as a module will be completely system dependent and often not required.
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written
by
Devon Ryan
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I do hope you took a look at this post: Sra Format Questions: How To Get A Sam File That Can Be Converted To Bam?