I had this problem too, my solution was to use unix command to trim and fold the fasta file. You would have to cut the header first, and catenate it with your sorted fasta file. It perfectly solves the problem.
Writing a shell script may be a good idea to make things easlier.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
This bioperl snippet fixes the fasta:
Code:use Bio::SeqIO; $in = Bio::SeqIO->new(-file => "inputfilename", -format => 'Fasta'); $out = Bio::SeqIO->new(-file => ">outputfilename", -format => 'Fasta'); while ( my $seq = $in->next_seq() ) {$out->write_seq($seq); }
Leave a comment:
-
I am having this same issue. While I have verified that there are lines of different length in the sequence file, however, why should this matter?
Leave a comment:
-
Originally posted by baohua100 View Postpopulus@Rust:~/samtools-0.1.5c_x86_64-linux$ ./samtools faidx /media/Poplar/baohua/genome/poplar_genome.fa
[fai_build_core] different line length in sequence 'scaffold_28'.
Segmentation fault
What's the meaning of defferent line length ?
It's the standard fasta file.
I download it from:
ftp://ftp.jgi-psf.org/pub/JGI_data/P...asked.fasta.gz
Leave a comment:
-
samtools faidx Segmentation fault
populus@Rust:~/samtools-0.1.5c_x86_64-linux$ ./samtools faidx /media/Poplar/baohua/genome/poplar_genome.fa
[fai_build_core] different line length in sequence 'scaffold_28'.
Segmentation fault
What's the meaning of defferent line length ?
It's the standard fasta file.
I download it from:
ftp://ftp.jgi-psf.org/pub/JGI_data/P...asked.fasta.gzTags: None
Latest Articles
Collapse
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
-
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 -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
32 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
35 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
29 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
53 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Leave a comment: