User: peri.tobias

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Posts by peri.tobias

<prev • 5 results • page 1 of 1 • next >
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nucleotide Hidden Markov Model search
... I am using HMMER v3.1 for nucleotide Hidden Markov Model searches. What I can't find in the manual is whether the hmm (I am building species-specific domain specific hmm) used to search a database looks at the plus and minus strand of the sequences in the database. To clarify - when running a BLAS ...
nhmmer hmmer written 16 months ago by peri.tobias0 • updated 15 months ago by Biostar ♦♦ 20
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Comment: C: Making bed files from fasta
... Thanks Matt. Yes I should have looked a bit closer before posting. ...
written 20 months ago by peri.tobias0
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Answer: A: Making bed files from fasta
... My apologies, my biopython script was corrupted. The fasta is okay. ...
written 20 months ago by peri.tobias0
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Making bed files from fasta
... Trying to run a biopython script in Windows cmd to make a bed file from a draft genome downloaded from NCBI. I get the following error. The headers appear to be fine. I have used the biopython script many times with success previously. Can someone see what the error is please? C:\Python34>p ...
genome written 20 months ago by peri.tobias0 • updated 18 months ago by Matt Shirley8.1k
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What happens to intermediate Trinity files when assembly terminated pre-completion
... I am assembling de novo transcriptomes using Trinity 2.1.1 on high performance computer cluster at my institution. My initial assembly ran out of wall-time at 65 hours. I left the intermediate files/folders within the directory and re-ran the assembly which completed in 6 hours. I would like to kno ...
trinity rna-seq written 2.0 years ago by peri.tobias0 • updated 7 months ago by Biostar ♦♦ 20

Latest awards to peri.tobias

Popular Question 8 months ago, created a question with more than 1,000 views. For Making bed files from fasta
Scholar 20 months ago, created an answer that has been accepted. For A: Making bed files from fasta

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