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Old 05-18-2016, 06:38 AM   #3
heso
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Location: Sweden

Join Date: May 2014
Posts: 19
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Quote:
Originally Posted by Michael.Ante View Post
Hi Heso,

You can use RSeQC's bam2fq.py to make a fastq file out of your "out_no_feature.sam".
In order to get the header into your files, use:
Code:
samtools view -SH original.sam > header.txt
Then use something like:
Code:
cat header.txt out_no_feature.sam | samtools view -bSh - > out_no_feature.bam
. In case it was not sorted according to the position, you may need to include a samtools sort into the pipe.
The "XF:Z"-field does not influence the downstream analysis. But since you have only alignments with this field will not give you any further information.

Cheers,
Michael

Thanks Michael, it worked perfectly!!

/Helena
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