Question: counting the unmapped reads
0
gravatar for A
4.8 years ago by
A3.7k
A3.7k wrote:

hi all,

i have a sam file, my supervisor asked me to count the number of unmapped reads, which command i should use ??

samtools view -c -F 4  [file.sam] says that input is probably trancuated

rna-seq • 1.5k views
ADD COMMENTlink modified 4.8 years ago by amirmhzadeh70 • written 4.8 years ago by A3.7k

ok thank you

ADD REPLYlink written 4.8 years ago by A3.7k
0
gravatar for Devon Ryan
4.8 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

Your command is fine, the file isn't. Ask your supervisor to double check that the file isn't corrupt.
 

ADD COMMENTlink written 4.8 years ago by Devon Ryan94k

Devon,

he just waiting the result i cant report any error...

ADD REPLYlink written 4.8 years ago by A3.7k
2

The file is corrupt, you can't give him a reliable result.
 

ADD REPLYlink written 4.8 years ago by Devon Ryan94k
1

If you've downloaded the file from somewhere you can try downloading again.

ADD REPLYlink written 4.8 years ago by atcg10
0
gravatar for amirmhzadeh
4.8 years ago by
amirmhzadeh70
Canada, Vancouver
amirmhzadeh70 wrote:

Your file is corrupt my friend. As mentioned above, the command in fine.
 

ADD COMMENTlink written 4.8 years ago by amirmhzadeh70

are you Iranian Amir???

ADD REPLYlink written 4.8 years ago by A3.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2043 users visited in the last hour