User: saanasum

gravatar for saanasum
saanasum10
Reputation:
10
Status:
New User
Location:
Last seen:
9 months ago
Joined:
9 months ago
Email:
f**************@uniklinikum-dresden.de

Posts by saanasum

<prev • 6 results • page 1 of 1 • next >
0
votes
2
answers
484
views
2
answers
Comment: C: Remove/Delete unique reads from a DNA fasta file
... Exactly, using -d a new file containing only duplicate reads will be generated. Therefore, in this file all unique reads are deleted. I can proceed working with this new file. As batch in bash: for i in *.fasta; do cat $i | seqkit rmdup -s -i -m -d "$i""_unique-reads-removed"; done ...
written 9 months ago by saanasum10
2
votes
2
answers
484
views
2
answers
Answer: A: Remove/Delete unique reads from a DNA fasta file
... Thanks @finswimmer for the suggestion of using [seqkit][1]. It is possible as described here: [seqkit rmdup][2]. When using **-d** a file containing the duplicated reads can be specified. Using a for loop in bash should enable automation for millions of fasta files. [1]: https://bioinf.shenwei ...
written 9 months ago by saanasum10
0
votes
2
answers
484
views
2
answers
Comment: C: Remove/Delete unique reads from a DNA fasta file
... However, *seqkit* might be the right choice when using the *rmdup* command and with **-d** parameter. [seqkit rmdup][1] [1]: https://bioinf.shenwei.me/seqkit/usage/#rmdup ...
written 9 months ago by saanasum10
0
votes
2
answers
484
views
2
answers
Comment: C: Remove/Delete unique reads from a DNA fasta file
... I guess this is an excellent solution for finding common sequences between two or more files (I tried it). However, I just want to extract sequences that occur at least two times within ONE file containing many fasta sequences (OR even better: to remove unique sequences in ONE fasta file). Finally, ...
written 9 months ago by saanasum10
0
votes
1
answer
742
views
1
answers
Answer: A: R packages for Data mining or machine learning of a set of differentialy express
... Maybe this helps to find a possible package: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5633036/ ...
written 9 months ago by saanasum10
4
votes
2
answers
484
views
5 follow
2
answers
Remove/Delete unique reads from a DNA fasta file
... I have millions of fasta files each containing many DNA sequences. I want to batch remove/delete reads (DNA sequences) that are unique in each fasta file, respectively. I only want to keep duplicate reads that occur at least two times in each fasta file, respectively. Does anybody know a command ...
fasta unique reads remove dna written 9 months ago by saanasum10 • updated 9 months ago by genomax73k

Latest awards to saanasum

Scholar 9 months ago, created an answer that has been accepted. For A: Remove/Delete unique reads from a DNA fasta file

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2591 users visited in the last hour