User: O.rka

gravatar for O.rka
O.rka210
Reputation:
210
Status:
Trusted
Location:
Website:
https://soundcloud.com...
Last seen:
2 months ago
Joined:
4 years, 4 months ago
Email:
j**********@gmail.com

Posts by O.rka

<prev • 214 results • page 1 of 22 • next >
0
votes
1
answer
157
views
1
answer
What is an easy-to-use `conda` installable method for annotating proteins for eukaryotes?
... I have a bunch of fragmented eukaryotic proteins that I would like to annotate. I don't have the genome so I can't use MAKER or FUNANNOTATE to build good gene models. I ran rnaspades for a de-novo transcriptome assembly and then prodigal for fragmented ORFs (yes, I know this is for prokaryotes). ...
genome annotation proteins eukaryotes written 9 weeks ago by O.rka210 • updated 9 weeks ago by Mensur Dlakic7.0k
0
votes
0
answers
174
views
0
answers
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 11 weeks ago by O.rka210
0
votes
0
answers
174
views
0
answers
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 11 weeks ago by O.rka210 • updated 11 weeks ago by geek_y11k
1
vote
1
answer
121
views
1
answer
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 4 months ago by O.rka210 • updated 4 months ago by WouterDeCoster44k
0
votes
0
answers
172
views
0
answers
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 5 months ago by O.rka210
0
votes
0
answers
117
views
0
answers
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 6 months ago by O.rka210
0
votes
1
answer
416
views
1
answers
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 6 months ago by O.rka210
0
votes
1
answer
416
views
1
answers
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 6 months ago by O.rka210
2
votes
1
answer
416
views
1
answer
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 6 months ago by O.rka210 • updated 6 months ago by Mensur Dlakic7.0k
0
votes
1
answer
430
views
1
answers
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 6 months ago by O.rka210

Latest awards to O.rka

Popular Question 11 weeks 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 3 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 3 months ago, created a question with more than 1,000 views. For Where to download gff3 file for EcoCyc data?
Great Question 5 months ago, created a question with more than 5,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Popular Question 5 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 6 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Popular Question 7 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Popular Question 8 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Epic Question 9 months ago, created a question with more than 10,000 views. For How to tell bloodtype from SNPs data?
Popular Question 10 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Voter 10 months ago, voted more than 100 times.
Scholar 10 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 11 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 12 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Popular Question 16 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Scholar 18 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 18 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Scholar 19 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
Centurion 19 months ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1728 users visited in the last hour