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Old 03-29-2016, 05:14 PM   #1
imsharmanitin
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Exclamation Chrom Sizes for Ensembl Reference

i want to convert BAM to BigWig for ensembl reference genome (Homo_sapiens.GRCh38.81.fa to be specific) using the following work flow.

Workflow:
# 1. Convert SAM to BAM
samtools view -S -b -o sample.bam sample.sam
# 2. Sort the BAM file
samtools sort sample.bam sample.sorted
# 3. Create BedGraph coverage file
genomeCoverageBed -bg -ibam sample.sorted.bam -g chromsizes.txt > sample.bedgraph
# 4. Convert the BedGraph file to BigWig
bedGraphToBigWig sample.bedgraph chromsizes.txt sample.bw

However, I am not sure how to get chromsizes.txt.

One suggested in a forum in biostars https://www.biostars.org/p/97890/ is by by running samtools faidx on the file and look at the .fai file.

i used this command

samtools faidx Homo_sapiens.GRCh38.81.fa

But this doesn't seem to work for me as I got .fai file with this output and it doesn't make any sense.

0 1657 58 60 61
1 632 1837 60 61
2 1351 2634 60 61
3 68 4042 60 61
4 712 4170 60 61
5 535 4940 60 61
6 138 5518 60 61
7 1187 5717 60 61
8 590 6970 60 61
9 840 7604 60 61
10 940 8493 60 61
11 918 9484 60 61
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Old 03-29-2016, 05:33 PM   #2
Richard Finney
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Look here:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/

Specifically
http://hgdownload.cse.ucsc.edu/golde...38.chrom.sizes
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Old 03-29-2016, 05:35 PM   #3
imsharmanitin
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Richard thanks a ton

Nitin
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Old 03-30-2016, 02:25 AM   #4
imsharmanitin
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One more query will the chromosome sizes, mentioned in links present in the quoted text, will be same for all the releases of GRCh38 i.e. GRCh38.76 which was first one to GRCh38.84 the latest one?

I would like to point out that I have used Homo_sapiens.GRCh38.81.fa

Best,
Nitin
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Old 03-30-2016, 02:37 AM   #5
Michael.Ante
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Hi Nitin,

the chromosome sizes don't change between the "minor changes". Only the gene and transcript annotation differs.

Cheers,
Michael
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Old 03-30-2016, 02:39 AM   #6
imsharmanitin
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Quote:
Originally Posted by Michael.Ante View Post
Hi Nitin,

the chromosome sizes don't change between the "minor changes". Only the gene and transcript annotation differs.

Cheers,
Michael
Michael, thanks for the clarification.

Cheers,
Nitin
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