bed graph and IGV
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2.6 years ago
Morris_Chair ▴ 260

Hello everyone,

I’m new to Chip-Seq data analysis and I’m using the Biostar handbook as reference which I find very useful. I understand that once I have the indexed bam file I can load it on IGV for peak detection but I can also use a smaller bed graph file to display coverages over intervals.

I used this command to create a bedgraph file but when I load it into IGV does not show any peak unlike the relative bam file

bedtools genomecov -ibam /SRR3033154_1.bam -g REF/saccer3.fa.fai  -bg > SRR3033154_1.bedgraph


I wonder what it could be wrong since I followed the book tutorial step by step (I think..)

thank you

Chip-seq biostar handbook • 1.0k views
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hi , are you sure it's REF/saccer3.fa.fai and not REF/saccer3.fa or just REF/saccer3?

Best

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-g expects a genome file. See for example Bedtools Genomecoveragebed Usage : How To Create A Genome File?
It is probably not required for a bam file though.

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Hi Titus, yes this is what I get from that file

cat saccer3.fa.fai
chrI    230218  6       50      51
chrII   813184  234836  50      51
chrIII  316620  1064292 50      51
chrIV   1531933 1387252 50      51
chrIX   439888  2949831 50      51
chrM    85779   3398523 50      51
chrV    576874  3486024 50      51
chrVI   270161  4074443 50      51
chrVII  1090940 4350016 50      51
chrVIII 562643  5462784 50      51
chrX    745751  6036686 50      51
chrXI   666816  6797360 50      51
chrXII  1078177 7477521 50      51
chrXIII 924431  8577271 50      51
chrXIV  784333  9520199 50      51
chrXV   1091291 10320226        50      51
chrXVI  948066  11433351        50      51


This is the command line from the book

Bedtools genomecov -ibam bam/SRR3033154.bam -g \$REF.fai -bg > bam/SRR3033154.bedgraph


Thank you

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Please use ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your reaction but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

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problem solved,

thank you all

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Hi Genomax, basically I didn't write correctly the command line below...I was a bit ashamed to tell..

bedtools genomecov -ibam /SRR3033154_1.bam -g REF/saccer3.fa.fai  -bg > SRR3033154_1.bedgraph


was missing -bg..

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nothing to be ashamed of, typos/omissions are the bane of every coder's existence