User: rmartson

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rmartson20
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Posts by rmartson

<prev • 30 results • page 1 of 3 • next >
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Comment: C: Show Progress (Bar?) For Blast+ Query
... Hello, is there any way this could be rewritten for outfmt = 7 tabular format with comments? ...
written 22 months ago by rmartson20
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Comment: C: Which database should I be downloading to setup local BLAST and BLAT to find hit
... Hey, I appreciate your help on my other question. I have the hg38.fa database file and can run BLAT searches on it now. However, the psl2bed script you recommended returns a "segmentation fault" error /usr/local/bin/psl2bed: line 140: 7344 Segmentation fault: 11 ${cmd} ${options} - 0<& ...
written 22 months ago by rmartson20
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Comment: C: Is there a more efficient way of checking multiple sequences for how many hits t
... psl2bed gives me this /usr/local/bin/psl2bed: line 140: 7344 Segmentation fault: 11 ${cmd} ${options} - 0<&0 ...
written 22 months ago by rmartson20
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Comment: C: Is there a more efficient way of checking multiple sequences for how many hits t
... [Had a problem but fixed it] ...
written 22 months ago by rmartson20
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Comment: C: Is there a more efficient way of checking multiple sequences for how many hits t
... Thanks for all the info but I ended up installing BLAT and downloading the hg38 assembly already. It probably just took much longer without all the info in one place. Any idea which set of fasta files in my "chroms" folder I should now be running BLAT against and how? I'm guessing there are a lot o ...
written 22 months ago by rmartson20
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Database for local BLAST and BLAT for 200-1000bp query sequences in human and primates
... I've installed BLAST and BLAT on my computer (OSX) but am confused with how many different files there are to download to set up a database on my computer and how to go about it. Can I use one with both BLAST and BLAT? Should I get the partially non-redundant database? ...
blast blat written 22 months ago by rmartson20 • updated 22 months ago by WouterDeCoster39k
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Comment: C: How to efficiently find any instances of two hits (LTRs) in close proximity to o
... Yes, one reference genome file (many complete sequences) and one aligned sequences file both in fasta format as you said. This whole thing would be much easier if there were some format of BLAST output that gave complete sequences as well as the locations of hit starts. The best I get is the locati ...
written 22 months ago by rmartson20
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How to efficiently find any instances of two hits (LTRs) in close proximity to one another in the genome? (Finding full-length proviruses)
... So I need to find any instances where two LTRs are within a certain distance of each other in the genome. I started Python recently and wrote the first thing I could think of that would achieve this purpose. It's a very stupid way of going about it, I think. It uses three for loops to first find an ...
biopython blast written 22 months ago by rmartson20
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Comment: C: Is there a more efficient way of checking multiple sequences for how many hits t
... 200bp Wouldn't I need to download the entire human genome? I have the space, actually. I just have no idea how to go about it. That sounds ideal though. ...
written 22 months ago by rmartson20
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Is there a more efficient way of checking multiple sequences for how many hits they have in the human genome?
... Currently I'm running a blast search for each flank sequence and then waiting to get the number of hits so they can be filtered into or out of a new file. There's probably a way to run multiple BLAST searches simultaneously, right? I'm just not sure how it would be done. """This script BLASTs ...
biopython blast written 22 months ago by rmartson20 • updated 22 months ago by Alex Reynolds28k

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