SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
SAM/BAM format to wiggle format pinki999 Bioinformatics 19 08-12-2015 12:35 AM
From bam to wig format mhadidi2002 Bioinformatics 1 02-17-2012 03:26 AM
Understanding BAM format. Joker!sAce Genomic Resequencing 7 03-16-2011 06:55 PM
How can I transfer txt file format NGS data ips Bioinformatics 3 03-10-2011 06:24 AM
Quality format in .bam slakov Illumina/Solexa 6 03-09-2011 05:30 AM

Reply
 
Thread Tools
Old 08-21-2010, 07:45 PM   #1
wuhoucdc
Member
 
Location: Nashville

Join Date: Oct 2009
Posts: 14
Default Transfer a whole genome with .bam format

Dear all,

Do you have experience to transfer a whole genome of short-reads with ~35X sequenced by Illumina GA to .bam format using samtools? I feel very strange when I got more than 500G data. I addition, how can you extract chromosomes one by one and sort as well as index them? Thank you very much!

Wuhoucdc
wuhoucdc is offline   Reply With Quote
Old 08-21-2010, 10:42 PM   #2
dawe
Senior Member
 
Location: 4530'25.22"N / 915'53.00"E

Join Date: Apr 2009
Posts: 258
Default

Quote:
Originally Posted by wuhoucdc View Post
Dear all,

Do you have experience to transfer a whole genome of short-reads with ~35X sequenced by Illumina GA to .bam format using samtools? I feel very strange when I got more than 500G data. I addition, how can you extract chromosomes one by one and sort as well as index them? Thank you very much!

Wuhoucdc
Never had a whole genome with that coverage :-( Sorted BAM may be slightly smaller.
To extract a single chrom (or a single region) index it

Code:
samtools index file.bam
and then extract your region

Code:
samtools view file.bam chrom[:start-end]
HTH

d
dawe is offline   Reply With Quote
Old 08-22-2010, 12:16 PM   #3
wuhoucdc
Member
 
Location: Nashville

Join Date: Oct 2009
Posts: 14
Default

Thanks for your answer, dawe.

But why did you say "Never had a whole genome with that coverage "? Most of the sequenced individuals such as YH (PMID:18987735) and AK1 (PMID:19587683) were higher than that coverage (>35X).

Wuhoucdc

Last edited by wuhoucdc; 08-22-2010 at 01:03 PM.
wuhoucdc is offline   Reply With Quote
Old 08-22-2010, 01:39 PM   #4
dawe
Senior Member
 
Location: 4530'25.22"N / 915'53.00"E

Join Date: Apr 2009
Posts: 258
Default

Quote:
Originally Posted by wuhoucdc View Post
Thanks for your answer, dawe.

But why did you say "Never had a whole genome with that coverage "? Most of the sequenced individuals such as YH (PMID:18987735) and AK1 (PMID:19587683) were higher than that coverage (>35X).

Wuhoucdc
:-) I usually deal with ChIP-seq or exome analysis, never had a "first hand" high coverage of human genome.
d
dawe is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:12 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO