User: A Soggy Waffle

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Posts by A Soggy Waffle

<prev • 15 results • page 1 of 2 • next >
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Comment: C: NCBI ORFfinder - How Does It Work
... I guess I wasn't clear enough. It's not the arguments and calling the program that's the problem. I want to know how it finds ORFs, algorithmically. ...
written 7 months ago by A Soggy Waffle0
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NCBI ORFfinder - How Does It Work
... NCBI help desk hasn't been very helpful to me on this so far. I'm looking for any record or docs on the ORFfinder tool. I want to know how it finds ORFs. Not how to use it, but how it determines what is and is not an ORF. Is it regex, HMM, fairy dust? Maybe such docs are posted somewhere but I can ...
ncbi written 7 months ago by A Soggy Waffle0 • updated 7 months ago by h.mon28k
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Comment: C: How to best get ALL Bacterial proteins from NCBI
... Just occurred to me to ask: What would be the difference between the blast index filtered for bacteria and all of the RefSeq bacterial protein faa files? ...
written 9 months ago by A Soggy Waffle0
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Comment: C: How to best get ALL Bacterial proteins from NCBI
... This may be a good backup to using the nr_v5 database. ...
written 9 months ago by A Soggy Waffle0
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Comment: C: How to best get ALL Bacterial proteins from NCBI
... I may try this. I am looking for the most sequences possible right now, not just RefSeq. ...
written 9 months ago by A Soggy Waffle0
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How to best get ALL Bacterial proteins from NCBI
... Hey all, I already have a head start on this question (following [this tutorial][1].) However that method is taking a _really_ long time since I have a list of ~0.5 Billion sequences to get. Additionally, some of my threads during sequence filtering are throwing errors and I'm afraid this method mi ...
protein big data written 9 months ago by A Soggy Waffle0 • updated 9 months ago by Carambakaracho1.9k
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Suspiciously Few Variants in BLAST Target Sequence?
... Hi all, I am trying to extract a gene sequence from 50 S. aureus WGS (from [https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP098767][1]) in order to test for positively selected sites in dihydropteroate synthase. In brief, I align them using bwa against the reference found in the study, call varian ...
sequence written 16 months ago by A Soggy Waffle0 • updated 16 months ago by h.mon28k
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Tools to enumerate amino acid mutations per site?
... Hi all, I could make a python script to do this for me but I'd rather be lazy and use a tool if it already exists. What I want to do is enumerate the various amino acid mutations at each position of a multiple sequence alignment. E.G. the first sequence is the reference. **INPUT** >seq1 ...
sequence written 17 months ago by A Soggy Waffle0 • updated 17 months ago by Pierre Lindenbaum124k
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(Closed) Your chrM is shorted than your reference chrM: Variant Calling
... I'm trying to run Torrent Variant Caller but run into an error > ERROR: Reference in BAM file does not match fasta file > Chromosome chrMin BAM has length 16569 while fasta has 16571 that fasta is my reference fasta. I'm stuck and don't know where to go from here. So far what I've tr ...
software error written 21 months ago by A Soggy Waffle0
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Comment: C: Invalid BAI magic number - TorrentVariantCaller
... I tried running the command from the dir with torrent_variant_caller.py and using symlinks to the BAM files but I just get the same error. The files definitely exist, running hexdump on the symlinks works. I'm contemplating finding a way to just edit the BAI magic numbers myself, since from https:/ ...
written 21 months ago by A Soggy Waffle0

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For NCBI ORFfinder - How Does It Work

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