I want to use BowTie. I download it and run the example commands given into it. However, I want to build index for read length 150 bps. This command (/.bowtie-build chromosome1.fa bowtieIndex ) seems gives default index bilder means for 36 bps. Can anybody help me how to build BowTie index for 150 bps.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
-
I'm no expert, but ... I think ..
The index built for your genome (or chromosome) should be able to handle varying sized read lengths as input to bowtie when doing alignment. The index is not specific to the read lengths that you are trying to align.
The introduction in the bowtie documentation mentions an example 36bp test file. The build is not made from this test file, it's just test data made from the genome (or chromsome). If you need 150bp test data ... well, that's another problem ... likely requiring a little custom scripting.
-
You build the index for the reference genome (and not for a particular type/length of reads).
I think you may be confused by the wording in the first para here (http://bowtie-bio.sourceforge.net/ma...what-is-bowtie). The 36-bp is a historical reference to the original read length for illumina reads (which have since been lengthened to 150 bp or more).Last edited by GenoMax; 06-19-2012, 08:19 AM.
Comment
-
index for viral genome
I want to run TopHAt of viral genome but to make it compatible I guess I need to generate index could some one guide me how can I generate such index files. Is there any web based tool or it is just only possibly only by programming. The particular genome is not available of tophat/ bowtie web page.
Thanks
Comment
-
Originally posted by mathew View PostI want to run TopHAt of viral genome but to make it compatible I guess I need to generate index could some one guide me how can I generate such index files. Is there any web based tool or it is just only possibly only by programming. The particular genome is not available of tophat/ bowtie web page.
Thanks
For Tophat2: http://bowtie-bio.sourceforge.net/bo...-build-indexer
Comment
Latest Articles
Collapse
-
by seqadmin
The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
Channel: Articles
07-08-2024, 03:19 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:46 AM
|
0 responses
9 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:46 AM
|
||
Started by seqadmin, 07-24-2024, 11:09 AM
|
0 responses
26 views
0 likes
|
Last Post
by seqadmin
07-24-2024, 11:09 AM
|
||
Started by seqadmin, 07-19-2024, 07:20 AM
|
0 responses
160 views
0 likes
|
Last Post
by seqadmin
07-19-2024, 07:20 AM
|
||
Started by seqadmin, 07-16-2024, 05:49 AM
|
0 responses
127 views
0 likes
|
Last Post
by seqadmin
07-16-2024, 05:49 AM
|
Comment