Linked Questions
16 questions linked to/from How to convert fasta file to tab delimited file
19
votes
7
answers
18k
views
9
votes
10
answers
25k
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.
<...
- 385
1
vote
4
answers
663
views
Removing particular line along with Fasta header in fasta file
I have a fasta file of 3'UTR sequences of the genes. Some of the gene do not have a 3'UTR sequence and reported with sequence unavailable but there is FASTA header.
...
- 19
1
vote
4
answers
973
views
Remove sequences from a fasta file with IDs from a text file using Python
a python beginner here.
I have a fasta file with 2500+ sequences, and after doing some analysis I want to remove around 200+ sequences based on the matching IDs. Now, I have one fasta file (as sample....
- 81
3
votes
2
answers
1k
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:
...
- 41
1
vote
3
answers
2k
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 ...
- 965
1
vote
3
answers
2k
views
Concatenate multiple fasta files into one file for MLST
I have seven fasta files, one per gene, with more than 400 fasta entries per file, like this:
Input:
Gene1.fasta
...
- 11
1
vote
6
answers
418
views
How to remove duplicates from a fasta file using python
I am using the following command:
...
2
votes
1
answer
851
views
How to concatenate FASTAs with respect to chromosome?
I have the following two small FASTAs, dna1.fa and dna2.fa:
...
- 1,423
3
votes
2
answers
720
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 ...
- 361
2
votes
1
answer
428
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 ...
- 393
2
votes
1
answer
328
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 ...
- 33
0
votes
1
answer
132
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.
...
- 115
2
votes
1
answer
70
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
2
answers
48
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 ...
- 29