Question: BED TO BAM INDEXING
0
gravatar for shambyross
3 months ago by
shambyross10
shambyross10 wrote:

Hello I have encountered a problem when trying to create bam index file.

The whole purpose of this is to convert .BED file into .BAM to visualize in IGB.

bedToBam -i input.bed -g hg19.txt > input.bam

samtools index _Specific_Peaks.bam *_Specific_Peaks.bai [E::hts_idx_push] chromosome blocks not continuous samtools index: failed to create index for "**_Specific_Peaks.bam"

I did sort the reference hg19.txt - chromosome size.

Can someone suggest what I am doing wrong? is there another tool to visualize .BED files?

Thank you

Fir

Thank you

bam • 122 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by shambyross10
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

It looks as if you are processing the data line command (not in Galaxy)? This forum is for Galaxy usage, but I would suggest sorting your BAM file by chromosome & coordinate. Use Samtools or Picard (both also have the sort functions wrapped in Galaxy). This may or may not work - it is a test.

For line command issues with Bedtools, you could also ask/search prior Q&A for usage/errors at the BedTools google group, or a general bioinformatics forum such as https://www.biostars.org/.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson23k
0
gravatar for shambyross
3 months ago by
shambyross10
shambyross10 wrote:

Hi Jen,

I just viewed in the UCSC genome browser.

Thank you for your help and suggestions.

ADD COMMENTlink written 3 months ago by shambyross10

Good choice on the alternative - it is very simple to just link over to UCSC (if they host your genome).

Very glad this was worked out and thanks for posting back! Jen

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson23k
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 16.09
Traffic: 97 users visited in the last hour