User: Bwremjoe

gravatar for Bwremjoe
Bwremjoe20
Reputation:
20
Status:
New User
Location:
Last seen:
2 weeks ago
Joined:
1 month ago
Email:
v******@evolbio.mpg.de

Posts by Bwremjoe

<prev • 10 results • page 1 of 1 • next >
1
vote
2
answers
213
views
2
answers
Answer: A: Blastn raw illumina reads all-against-all and return only non-hits
... For anyone returning to this in the future, there's a biopython tutorial on doing exactly this, in a much more efficient way: https://biopython.org/wiki/Retrieve_nonmatching_blast_queries ...
written 15 days ago by Bwremjoe20
0
votes
2
answers
213
views
2
answers
Comment: C: Blastn raw illumina reads all-against-all and return only non-hits
... Yes, that definitely speeds things a lot, thank you. =) ...
written 26 days ago by Bwremjoe20
0
votes
2
answers
213
views
2
answers
Comment: C: Blastn raw illumina reads all-against-all and return only non-hits
... I'll give that a try, thank you =) ...
written 26 days ago by Bwremjoe20
0
votes
2
answers
213
views
2
answers
Comment: C: Blastn raw illumina reads all-against-all and return only non-hits
... Ah, that makes sense. Thank you. ...
written 29 days ago by Bwremjoe20
0
votes
2
answers
213
views
2
answers
Comment: C: Blastn raw illumina reads all-against-all and return only non-hits
... Yeah, but that still doesn't give me the sequence data, which is what I need. In the end, the blastn part is not the bottle neck right now, it's the grepping (which takes 3.5 days...) Anyway, thanks for your help genomax. ...
written 29 days ago by Bwremjoe20
0
votes
2
answers
213
views
2
answers
Comment: C: Blastn raw illumina reads all-against-all and return only non-hits
... So, do you think the stuff I do with gripping / sed is then the only way forward? (again, given that I have to use blastn... which is unfortunately true for now) It's very inefficient I think... ...
written 29 days ago by Bwremjoe20
0
votes
2
answers
213
views
2
answers
Comment: C: Blastn raw illumina reads all-against-all and return only non-hits
... I am confused as to what outfmt 7 shows... it says 0 hits found, but then it lists 1 hit, which is a perfect hit. Am I missing something? EDIT: Oh wait, that's two queries. But it doesn't give the sequence when no hit is found, right? ...
written 29 days ago by Bwremjoe20
0
votes
2
answers
213
views
2
answers
Comment: C: Blastn raw illumina reads all-against-all and return only non-hits
... I am definitely going to do this, but I'd like to try the blastn-approach nonetheless. It was used before, and like you, I'm not sure it's the best way to go. But in order to show this, I'd have to use blastn to repeat someone else's analysis. But thanks for the tip, I think that tool sounds like ...
written 29 days ago by Bwremjoe20
0
votes
2
answers
213
views
2
answers
Comment: C: Blastn raw illumina reads all-against-all and return only non-hits
... I am using blast purely because I am reproducing someone's method and trying to compare it to other approaches (like a NGS aligner, as you say). I think outfmt 7 does in fact NOT include missed hits. Not sure about 17 though. ...
written 4 weeks ago by Bwremjoe20
7
votes
2
answers
213
views
2
answers
Blastn raw illumina reads all-against-all and return only non-hits
... Dear Biostars folk, I have been trying to come up with an efficient way to return all the NON-hits from a blastn query. Basically, I need to blast all reads in an Illumina library against one another, and only find the reads in set A that have not hit in B. Although I have a solution, it seems to b ...
illumina reads blast blastn written 4 weeks ago by Bwremjoe20

Latest awards to Bwremjoe

Scholar 15 days ago, created an answer that has been accepted. For A: Blastn raw illumina reads all-against-all and return only non-hits

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1132 users visited in the last hour