genome.info is empty

[Maarten-vd-Sande]

When I use the command you provided to generate the genome.info I end up with an empty genome.info. These are the first couple lines of the bam file:

samtools view -H /vol/atacpipeline/dedup/GSM2837484-Bl71nemr.bam | head
@HD	VN:1.5	SO:coordinate
@SQ	SN:FLLO01000001.1	LN:10571537
@SQ	SN:FLLO01000002.1	LN:9833161
@SQ	SN:FLLO01000003.1	LN:8797521
@SQ	SN:FLLO01000004.1	LN:8740412
@SQ	SN:FLLO01000005.1	LN:8020686
@SQ	SN:FLLO01000006.1	LN:7953648
@SQ	SN:FLLO01000007.1	LN:7634011
@SQ	SN:FLLO01000008.1	LN:7394200
@SQ	SN:FLLO01000009.1	LN:6209474

And when I run this no output is generated:

samtools view -H /vol/atacpipeline/dedup/GSM2837484-Bl71nemr.bam| perl -ne 'if(/^@SQ.*?SN:(\w+)\s+LN:(\d+)/){print $1,"\t",$2,"\n"}'

perl -v
This is perl 5, version 26, subversion 2 (v5.26.2) built for x86_64-linux-thread-multi 
...

What am I doing wrong?

[EvanTarbell]

Thanks for the comment and for using our tool.
You can try this command as well:

$ samtools view -H ExampleFile.sorted.bam | grep SQ | cut -f 2-3 | cut -d ':' -f 2 | cut -f 1 > tmp
$ samtools view -H ExampleFile.sorted.bam | grep SQ | cut -f 2-3 | cut -d ':' -f 2,3 | cut -d ':' -f 2 > tmp2
$ paste tmp tmp2 > genome.info; rm tmp tmp2

Let me know if that works.

[Maarten-vd-Sande]

Yes that works. Thanks