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3
votes
2
replies
650
views
How can I convert this pairwise format to fasta?
fasta python bash
updated 14 months ago by 141k • written 14 months ago by ▴ 170
0
votes
1
reply
458
views
Remove duplicates in multifasta, where entries are paired
bash python
updated 14 months ago by ★ 1.9k • written 14 months ago by ▴ 170
5
votes
3
replies
770
views
Tool for aligning short protein sequences
protein alignment
updated 15 months ago by 11k • written 15 months ago by ▴ 170
1
vote
2
replies
477
views
How to swap fasta entrys in a fasta file?
awk fasta bash sed
updated 15 months ago by 13k • written 15 months ago by ▴ 170
3
votes
3
replies
678
views
Bowtie2 not putting /2 /1 at the end of paired reads in SAM file
alignment bowtie
updated 15 months ago by 100k • written 15 months ago by ▴ 170
3
votes
1
reply
484
views
How to split fasta file by ID, making sure to keep two entrys in each file
fasta split seqkit bash
updated 15 months ago by 100k • written 15 months ago by ▴ 170
2
votes
3
replies
868
views
Extract alignment in fasta format from BAM/SAM file
alignment bam
updated 15 months ago by 100k • written 15 months ago by ▴ 170
6
votes
3
replies
759
views
Modifying FASTQ header
sed fastq awk
updated 18 months ago by ▴ 60 • written 19 months ago by ▴ 170
7
votes
4
replies
1.0k
views
Automating pipeline with Parallel, read files in separate folders
fastq automation bash parallel
updated 23 months ago by ★ 4.4k • written 23 months ago by ▴ 170
1
vote
2
replies
806
views
Replace fasta ID with value from TSV file (sed with special characters)
sed
updated 2.4 years ago by 21k • written 2.4 years ago by ▴ 170
1
vote
1
reply
637
views
Software/package that can visualise amino acid mutations against a reference genome
mutations visualisations
3.2 years ago by SaltedPork ▴ 170
0
votes
2
replies
1.1k
views
How to create coverage graph/plot for an entire Illumina run
coverage r bam graph plot
3.3 years ago by SaltedPork ▴ 170
0
votes
1
reply
853
views
Convert the NT position in a VCF file to an AA position
ivar vcf gff
3.6 years ago by SaltedPork ▴ 170
0
votes
3
replies
1.5k
views
Using GNU Parallel to read arguments into a bash script
gnu parallel bash
3.6 years ago by SaltedPork ▴ 170
1
vote
2
replies
5.7k
views
Having trouble with Seqkit Replace, trying to rename fasta headers from file
seqkit
updated 3.8 years ago by ★ 1.5k • written 4.2 years ago by ▴ 170
6
votes
7
replies
3.2k
views
Rename FASTA headers based on filename
bash
updated 4.9 years ago by ★ 2.2k • written 4.9 years ago by ▴ 170
16
votes
11
replies
3.2k
views
Rename fasta headers from CSV
bash perl python
updated 2.0 years ago by ★ 2.2k • written 4.9 years ago by ▴ 170
5
votes
10
replies
9.6k
views
Using BWA Index and i get 5 output files, but BWA-mem asks for just 1
bwa BWA bwa-index
updated 5.7 years ago by • 0 • written 7.6 years ago by ▴ 170
4
votes
7
replies
1.2k
views
How to get list of different bases and their positions from an alignment?
alignment
updated 6.0 years ago by 47k • written 6.0 years ago by ▴ 170
0
votes
0
replies
1.1k
views
In Jalview, how can I colour just the nucleotides that are different between sequences
alignment jalview
6.0 years ago by SaltedPork ▴ 170
33
votes
11
replies
11k
views
Getting a bash pipeline to output non-zero exit code when a step fails
bash command-line sh
updated 6.2 years ago by ★ 3.4k • written 6.2 years ago by ▴ 170
7
votes
4
replies
2.1k
views
How to convert string into fasta using bash?
fasta perl bash string
updated 6.2 years ago by 161k • written 6.2 years ago by ▴ 170
10
votes
8
replies
4.1k
views
Any ideas on converting IUPAC ambiguity codes in a fasta file
fasta iupac regex perl bash
updated 2.2 years ago by • 0 • written 6.2 years ago by ▴ 170
0
votes
3
replies
1.5k
views
Jalview crashes when I resize window, any fixes?
jalview
updated 6.2 years ago by ▴ 100 • written 7.5 years ago by ▴ 170
11
votes
9
replies
2.8k
views
Getting files from BaseMount (Using find command to loop through the symlinks)
basemount basespace
updated 6.2 years ago by ★ 3.5k • written 6.2 years ago by ▴ 170
3
votes
4
replies
2.4k
views
I'm putting a pipeline into docker, where do I store the tar files for my dependencies, on GitHub or within the Docker image?
docker pipeline
updated 6.3 years ago by ★ 2.1k • written 6.3 years ago by ▴ 170
13
votes
7
replies
7.5k
views
How to split fasta by '>' into a file each containing one sequence, and have the name of that file be the ID?
fasta bash split
updated 6.3 years ago by 161k • written 6.3 years ago by ▴ 170
8
votes
4
replies
2.4k
views
How can I run lastz on multiple files using a bash loop and an associative array?
bash
updated 10 months ago by 43k • written 6.3 years ago by ▴ 170
5
votes
4
replies
3.5k
views
How can I split a fasta file into many files, one file for each ID line and its sequence
fasta split
updated 6.4 years ago by 141k • written 6.4 years ago by ▴ 170
4
votes
5
replies
1.6k
views
How can I calculate coverage from the base frequencies file?
coverage basefrequency frequency
updated 6.4 years ago by 21k • written 6.4 years ago by ▴ 170
15
votes
15
replies
3.1k
views
Printing specific sequence and ID from combined fasta file using bash commands
fasta bash
updated 6.4 years ago by 161k • written 6.4 years ago by ▴ 170
2
votes
2
replies
4.1k
views
How can I extract sequence from a SAM file, with coordinates
sam samtools
7.4 years ago by SaltedPork ▴ 170
1
vote
5
replies
1.7k
views
How can I assign sequence length to an ID in a FASTA file using Perl?
Perl fasta
updated 7.4 years ago by 14k • written 7.4 years ago by ▴ 170
3
votes
6
replies
2.2k
views
How do I extract read ID after using the Bedtools genome coverage tool?
bedtools coverage histogram
updated 7.5 years ago by 12k • written 7.5 years ago by ▴ 170
0
votes
0
replies
1.0k
views
How can I extract sequence from the human reference that maps to end sequences from FOSMIDs?
fosmid human reference
7.5 years ago by SaltedPork ▴ 170
3
votes
1
reply
3.4k
views
How can I use Samtools to map coverage distribution?
samtools coverage distribution
7.5 years ago by SaltedPork ▴ 170
5
votes
3
replies
2.8k
views
Parsing Read ID's out of a SAM file
SAM Perl Parsing
updated 7.5 years ago by 104k • written 7.5 years ago by ▴ 170
37 results • Page 1 of 1
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