Linked Questions

19
votes
7answers
9k views

How to convert FASTA to BED

I have a FASTA file: ...
8
votes
8answers
14k views

Remove/delete sequences by ID from multifasta

I have a fasta file like this: >Id1 ATCCTT >Id2 ATTTTCCC >Id3 TTTCCCCAAAA >Id4 CCCTTTAAA I want to delete sequences that have the following IDs. <...
1
vote
3answers
1k views

How to split multifasta based on partial fasta header

I have download a batch of refseq fasta files and want to split them based on strain. this is complicated by accession numbers, project IDs etc. I downloaded the genomes via eDirect from NCBI. I know ...
3
votes
2answers
629 views

How to find common sequences among 6 multi-fasta files

I have 6 multi-fasta files, every of them contains ca 1500 sequences like that: ...
2
votes
1answer
587 views

How to concatenate FASTAs with respect to chromosome?

I have the following two small FASTAs, dna1.fa and dna2.fa: ...
2
votes
1answer
196 views

How to generate a weblogo image that takes into account sequence frequencies?

I have a large aligned amino acid sequences file (fasta file) from next generation sequencing data. The unique sequences have been aligned but these all have certain read counts (frequencies ...
2
votes
1answer
145 views

how to merge two fasta based on full fasta header and remove the duplicate

I am wondering if anyone can help to merge two fasta file based on the full header as initially gene ID may be similar in some of the sequences and to remove the duplicate entry based on full fasta ...
2
votes
2answers
100 views

How to remove sequences from a fasta file using a sequence ID list which contains a space within the id?

I have a fasta file that contains sequence reads and sequence id file that needed to be removed from the fasta file. I have done this earlier, but since id contains a space my piece of code is not ...
0
votes
1answer
77 views

Subset a protein fasta based on sequence length?

I have a strange protein fasta file. There are several entries for the same gene and I need to extract the entry with the longest width. ...
2
votes
1answer
62 views

RNA seq fasta file annotation from alignment to reference matches

I've got a fasta file with some RNA seq data and another csv file with the output from plast where I've aligned it to a reference using plastn. I'm struggling with figuring out a command to append my ...
1
vote
2answers
44 views

Get & Annotation of isomiR (isoform of miRNA) profile from RNA-seq

I should get and analyse isomiR (isoform of miRNA) profile from RNA-seq with FASTA format. The best tool for this is "DeAnnIso". But here is a problem with this tool, it only allows you to upload ...