User: O.rka

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O.rka200
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Posts by O.rka

<prev • 213 results • page 1 of 22 • next >
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Comment: C: How to find all mapped locations of a read from PySam?
... I'm trying to do a complicated analysis based on read sizes and multimapping and I can't really do that in a bash shell. Doesn't the command above just output a single positoin ...
written 3 days ago by O.rka200
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How to find all mapped locations of a read from PySam?
... I have a mapping with an insane amount of multimapped reads. I'm trying to figure out all the locations these multimapped reads have mapped to but I'm having difficult accessing all of the locations from the bam file. I got my BAM file from STAR aligner. Here's my STAR command: conda activ ...
alignment written 3 days ago by O.rka200 • updated 3 days ago by geek_y11k
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How to calculate differential methylation from nanopore reads?
... I have 2 timepoint-specific conditions (`t=0` and `t=X`) and 12 specimens. I used [nanopolish](https://github.com/jts/nanopolish) to calculate methylation signatures per base, in particular, with this script: https://github.com/jts/nanopolish/blob/master/scripts/calculate_methylation_frequency.py ...
methylation sequencing written 6 weeks ago by O.rka200 • updated 6 weeks ago by WouterDeCoster44k
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What is the recommended way to subsample Oxford Nanopore (ONT) fastq reads with matching fast5?
... I want to run `nanopolish` and I have some large fastq files. I want to subsample them but I also need the fast5 for the subsampled reads. What is the best method to do this considering the size distributions of the ONT reads? ...
sequencing written 3 months ago by O.rka200
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What does it mean when "-" or "+" join KEGG orthologs in a KEGG module definition?
... I'm looking at [KEGG Module M00377](https://www.genome.jp/kegg-bin/show_module?M00377). I want to calculate how complete this module is in a query set of genes to calculate a module completion ratio [MCR] based on KEGG orthologs [KO]. The way I'm calculating the MCR is the following: p = KOs ...
annotation ortholog module metagenomics kegg written 4 months ago by O.rka200
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Comment: C: Why is hmmsearch only using the 1st HMM in a concatenated HMM database?
... Thanks again, I'll run some test examples right now. ...
written 4 months ago by O.rka200
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Comment: C: Why is hmmsearch only using the 1st HMM in a concatenated HMM database?
... > Description hmmsearch is used to search one or more profiles against a > sequence database. For each profile in hmmfile, use that query profile > to search the target database of sequences in seqdb, and output ranked > lists of the sequences with the most significant matches to the > ...
written 4 months ago by O.rka200
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Why is hmmsearch only using the 1st HMM in a concatenated HMM database?
... I'm running `hmmsearch via HMMER 3.3` with a concatenated HMM file. Here is the first 1000 lines of my [tigrfams.hmm.gz](https://pastebin.com/raw/Qt0PrqvV). It looks like the file is properly merged with the following format: [HMM] // [HMM] // I don't know why but I'm only getti ...
protein domain hmmer hmm script bash written 4 months ago by O.rka200 • updated 4 months ago by Mensur Dlakic6.0k
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Comment: C: How to choose between --cut_ga, --cut_tc, and --cut_nc in hmmsearch? (hmmer)
... Ok interesting, it might be a good idea if I start using `-Z 45638612` to keep analysis pipelines fairly consistent. My last question...is the `score` affected by `-Z` or only the `E-value` calculation? ...
written 4 months ago by O.rka200
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Comment: C: How to choose between --cut_ga, --cut_tc, and --cut_nc in hmmsearch? (hmmer)
... Thank you, this is extremely helpful. When you're saying database size do you mean the number of HMMs in an HMM database or the number of sequences used to create the database? Should I use the `-Z` flag used to build each PFAM individually for each hmmsearch run? For example, `PF10417.9` there ...
written 4 months ago by O.rka200

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Scholar 8 months ago, created an answer that has been accepted. For A: Can you assemble with merged paired end reads and unmatched reads as "single end
Popular Question 8 months ago, created a question with more than 1,000 views. For Gene ontology-type analysis but with protein domain IDs? (e.g. TIGRFAM, PFAM)
Popular Question 10 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Popular Question 13 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Scholar 15 months ago, created an answer that has been accepted. For A: Can you assemble with merged paired end reads and unmatched reads as "single end
Popular Question 15 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Scholar 16 months ago, created an answer that has been accepted. For A: Can you assemble with merged paired end reads and unmatched reads as "single end
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Popular Question 18 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?

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