Hello, a quick question for anybody familiar with bowtie. In my reference genome files, which have names like SVID_XXX, the first line of text, before the actual sequence data is a line like >Chromosome, or >ContigXXXX, .... In the bowtie output data, Chromosome or ContigXXXX shows up as the file name it mapped to instead of SVID_XXX, the actual file name. My question is this, is bowtie taking the > symbol in the first line of text as a command to redirect to this file name or whatever comes after it in that line? I know that > redirects output to a file, but why does this happen in bowtie since the file already has a file name, and > only shows up in the first line of a text file? I hope this makes sense, any thoughts?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Your reference genome files are FASTA files.
The FASTA file format is simple.
There is one line, starting with the symbol ">" which describes the sequence.
The first word after ">" is the name of the sequence.
Following the sequence description is the sequence itself.
Bowtie and all programs dealing with raw genomic data are written to be able to parse FASTA files.
The FASTA format has nothing to do with the Unix redirection operator, and dates back to 1985.Last edited by blancha; 11-13-2015, 07:50 PM.
Latest Articles
Collapse
-
by seqadmin
Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.
Somatic Genomics
“We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...-
Channel: Articles
05-24-2024, 01:16 PM -
-
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 -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Comprehensive Sequencing of Great Ape Sex Chromosomes Yields Insights into Evolution and Genetic Variability
by seqadmin
Started by seqadmin, Yesterday, 01:32 PM
|
0 responses
10 views
0 likes
|
Last Post
by seqadmin
Yesterday, 01:32 PM
|
||
Started by seqadmin, 05-24-2024, 07:15 AM
|
0 responses
199 views
0 likes
|
Last Post
by seqadmin
05-24-2024, 07:15 AM
|
||
Started by seqadmin, 05-23-2024, 10:28 AM
|
0 responses
221 views
0 likes
|
Last Post
by seqadmin
05-23-2024, 10:28 AM
|
||
Started by seqadmin, 05-23-2024, 07:35 AM
|
0 responses
232 views
0 likes
|
Last Post
by seqadmin
05-23-2024, 07:35 AM
|
Comment