I have a query file with 70,000 lines of sequences and when I do the
each sam output file is about 35 mb and obviously contains all the sequence lines. I need to perform the alignment on about 1000 files, so you can imagine that I don't want to have 35 gigs worth of output to sort.
I am trying to get rid of the non-aligned reads from the SAM output file ans I searched through forums and tried the following code with no avail.
All my sam files give the following error:
Here's what a part of my sam files looks like
I'd appreciate help with this!
Code:
bwasw
I am trying to get rid of the non-aligned reads from the SAM output file ans I searched through forums and tried the following code with no avail.
Code:
./samtools view -bS -f 4 testing.sam > output.bam
Code:
[samopen] SAM header is present: 1 sequences. [sam_read1] reference '0' is recognized as '*'. Parse warning at line 3: mapped sequence without CIGAR Parse error at line 3: missing colon in auxiliary data Aborted (core dumped)
Here's what a part of my sam files looks like
Code:
@SQ SN:gi|89106884|ref|AC_000091.1| LN:4646332 4 * 0 0 * * 0 0 <CGTAAAAAGGA> * 4 * 0 0 * * 0 0 <TAGCCGTAGGG> *
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