I have got some illumina data in a a merged BAM file for a particular sample and I would like to convert it back to per lane data files (BAM or fastq) so it would be compatible with the analysis pipeline. Any ideas on the best way to do this?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
When I did this a few days ago (with only knowledge of command-line stuff and samtools), here's a rough guide to what I did:- Extract header from BAM file
Code:
samtools view -H infile.bam > header.sam
- filter out lanes from BAM file, add header
Code:
(cat header.sam; samtools view infile.bam | grep '^DATA...._<lane>_.') > out_lane<lane>.sam
- convert SAM to BAM
Code:
samtools view -S out_lane<lane>.sam -b > out_lane<lane>.bam
There's probably some better way, but it would have taken longer for me to find than for me to just do it and deal with the additional overhead of storing temporary SAM files per lane.
- Extract header from BAM file
-
If the lane info is stored in RG tags you can use this: http://genome.sph.umich.edu/wiki/SplitBam
Comment
-
SplitBam looks ideal, but I can't find a download link for it. Any ideas?
And thanks for the other suggestion too, that makes a lot of sense.
--EDIT--
Actually it looks like there are no @RG in the headers ... Oh Dear.Last edited by danielsbrewer; 09-29-2011, 01:03 AM.
Comment
-
Originally posted by danielsbrewer View PostSplitBam looks ideal, but I can't find a download link for it. Any ideas?
And thanks for the other suggestion too, that makes a lot of sense.
--EDIT--
Actually it looks like there are no @RG in the headers ... Oh Dear.Originally posted by jtladner View PostI am trying to do the exact same thing and I do have @RG tags, but I can not find a download link for SplitBam. Does anyone know how to download this program?
Jason
Comment
-
Originally posted by jtladner View PostI am trying to do the exact same thing and I do have @RG tags, but I can not find a download link for SplitBam. Does anyone know how to download this program?
Jason
splitBam is part of the bamUtil package, which i found it here https://github.com/Homebrew/homebrew-science and it was very easy to download it.
Comment
Latest Articles
Collapse
-
by seqadmin
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
Channel: Articles
05-06-2024, 07:48 AM -
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 05-07-2024, 06:57 AM
|
0 responses
12 views
0 likes
|
Last Post
by seqadmin
05-07-2024, 06:57 AM
|
||
Started by seqadmin, 05-06-2024, 07:17 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
05-06-2024, 07:17 AM
|
||
Started by seqadmin, 05-02-2024, 08:06 AM
|
0 responses
22 views
0 likes
|
Last Post
by seqadmin
05-02-2024, 08:06 AM
|
||
Started by seqadmin, 04-30-2024, 12:17 PM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
04-30-2024, 12:17 PM
|
Comment