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Question: BED TO BAM INDEXING
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gravatar for shambyross
14 months ago by
shambyross • 10
shambyross • 10 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 • 582 views
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modified 14 months ago • written 14 months ago by shambyross • 10
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gravatar for Jennifer Hillman Jackson
14 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 14 months ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for shambyross
14 months ago by
shambyross • 10
shambyross • 10 wrote:

Hi Jen,

I just viewed in the UCSC genome browser.

Thank you for your help and suggestions.
ADD COMMENT • link written 14 months ago by shambyross • 10

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 REPLY • link written 14 months ago by Jennifer Hillman Jackson ♦ 25k
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