Does anyone know of a script that allows one to convert Qual scores from a fastq file in order to map w/ BWA or Bowtie using the command line? I'm familar with the Galaxy tools function, but Galaxy has really been unreliable lately, I'd love to move away from it whenever possible.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
The qual portion of fastq comes in different varieties. Bwa and bowtie only accept one format. The galaxy fastq groomer changes the qual score format to allow bwa or bowtie compatibility. I would like to run that script from the command line, and I wondered if anyone knew where to find it.
Comment
-
Originally posted by Giles View PostThe qual portion of fastq comes in different varieties. Bwa and bowtie only accept one format...
Code:bowtie: --phred-33 (default) or --phred-64 bwa aln: (default is Phred+33, no option required) or -I (Phred+64).
Comment
-
There are several other options for doing the conversion if you need to, e.g. EMBOSS seqret
Comment
Latest Articles
Collapse
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
-
by seqadmin
The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.
Avian Conservation
Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...-
Channel: Articles
03-08-2024, 10:41 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:37 PM
|
0 responses
12 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:37 PM
|
||
Started by seqadmin, Yesterday, 06:07 PM
|
0 responses
10 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:07 PM
|
||
Started by seqadmin, 03-22-2024, 10:03 AM
|
0 responses
52 views
0 likes
|
Last Post
by seqadmin
03-22-2024, 10:03 AM
|
||
Started by seqadmin, 03-21-2024, 07:32 AM
|
0 responses
68 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Comment