View Single Post
Old 05-18-2016, 03:41 AM   #2
Michael.Ante
Senior Member
 
Location: Vienna

Join Date: Oct 2011
Posts: 123
Default

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

Last edited by Michael.Ante; 05-18-2016 at 03:42 AM. Reason: Typo
Michael.Ante is offline   Reply With Quote