The unique tags number from parseAlignment.pl

[yang chen]

Hi Chaolin,

     I used STAR to do mapping. The unique mapped reads number is 12,327,003. The total input reads number before mapping is 45,444,421. 

     Then I used parseAlignment.pl to parse the sam file. It should only extract the unique mapping reads. But the row number in the $f.tag.bed are 52,458,286. It is much larger than the input reads number and the unique mapped read number in STAR. 

      Could you give me some suggestions? Thanks.      

Best regards,

Yang Chen 

[Huijuan Feng]

Hi Yang,

Could you provide your command line of using parseAlignment.pl here to help understand your problem? Thanks!

Best,

Huijuan

[yang chen]

Hi Huijuan,

    This is the command. Thanks very much. 

perl /usr/local/CTK/parseAlignment.pl -v --map-qual 1 --min-len 18 --mutation-file "$px".UMI.mutation.txt $of4 - | gzip -c > "$px".UMI.tag.bed.gz

Best regards,

Yang Chen 

[yang chen]

of4="$px"".UMI.sam.gz"

在 2020年2月24日星期一 UTC-5上午10:35:35，yang chen写道：

[Huijuan Feng]

Could you please share the sam file? Thanks!

Best,

Huijuan

[yang chen]

Hi Huijuan,

     Thanks very much. It's my problem. I find the read number after using is parseAlignment.pl  is 5,864,538. It is reasonable. 

Best regards,

Yang Chen