Question: Why samtools depth error
0
gravatar for 9521ljh
18 months ago by
9521ljh40
9521ljh40 wrote:

i have a bed file

cat AMP_region.bed
chr1    157543538       157567870
chr1    160313062       160328742
chr1    163291722       163325553
chr2    85360582        85537511



samtools depth -a -b AMP_region.bed test.bam

above command no output anything. what is wrong?

i already tried removing prefix 'chr', but empty output...

samtools depth -a -r 1:50246462-59249785 test.bam
1       50246462        69
1       50246463        69
1       50246464        69

it is work well

Thus i think bed file is something wrong..

sequencing sequence gene • 363 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by 9521ljh40

There you already have your answer. The chr prefix must be removed. Please show how you removed it in the first place (command line).

ADD REPLYlink written 18 months ago by ATpoint44k

i followed this command line:

sed 's/chr//' AMP_region.bed

cat AMP_region.bed
1    157543538       157567870
1    160313062       160328742
ADD REPLYlink written 18 months ago by 9521ljh40

This also output empty

ADD REPLYlink written 18 months ago by 9521ljh40
0
gravatar for 9521ljh
18 months ago by
9521ljh40
9521ljh40 wrote:

sorry, i solve this problem...

actually test.bam file is another directory. Thus i copy it in same directory ( bed, bam, bai)

ADD COMMENTlink written 18 months ago by 9521ljh40
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