I want to rename sequence headers

Question

[Riyad]

I have assembled transcript files with thousands of sequences with headers as like:

>TRINITY_DN50_c0_g2_i1 len=1961 path=[0:0-1960]
>TRINITY_DN59_c0_g1_i2 len=1961 path=[0:0-1960]

But, I want to rename them into as like:

>TRINITY_1
>TRINITY_2

Just all sequences will retain with TRINITY adding chronological number. Total number sequences are 40000

[LauferVA]

1. what file format ?

2. what programming language?

3. Have you stored the information in the header in a separate location?

[Michael]

In addition to what Mensur said, I would also state that renaming is not recommended because the string carries meaning. You will, for example, not be able to extract the longest isoform per gene from the edited file, and it will make reproducing subsequent analysis harder. Most tools should be able to deal with the Trinity identifiers. Unless a tool definitely does not support them, I would leave them as they are.

[Riyad]

Thanks@ Michael I appreciate this suggestions.

Answer 1

[Mensur Dlakic]

Many posters think that their problems are unique, but in most cases that's not true. Yours, in particular, is one of most frequently discussed problems. That means that searching for "rename fasta header" from the main page will give you numerous solutions.

https://www.biostars.org/post/search/?query=rename+fasta+header

[Riyad]

Thank@ Mensur

Answer 2

[Mark]

Use seqkit replace, assuming your file name is trinity.fasta:

seqkit replace trinity.fasta -p "(.+)" -r "TRINITY_{nr}" > trinity.renamed.fasta

Where:

• -p "(.+)" is the match pattern to match the whole header text
• -r "TRINITY_{nr}" is the replacement pattern, where {nr} adds the record number.

See https://bioinf.shenwei.me/seqkit/usage/#replace for more information

[Riyad]

Thanks@Mark Its working now with seqkit nicely. ....

[Mark]

Please mark the answer as correct.

Answer 3

[benformatics]

R version

library(Biostrings)  
fa <- readDNAStringSet('your.fasta')
names(fa) <- paste0('TRINITY_',seq(fa))
writeXStringSet(fa,'your_new.fasta',format='fasta')

Answer 4

[Hugo]

You can also use SEDA (https://www.sing-group.org/seda). Specifically, you would use the "Rename header" operation first, to keep the "TRINITY" part of the headers using the "Multipart header" rename type.

Then, you would use the "Rename header" again, but this time with "Add prefix/suffix" rename type to add the indexes.

We will soon release a new SEDA version that comes with a CLI.