User: O.rka

gravatar for O.rka
O.rka80
Reputation:
80
Status:
Trusted
Location:
Website:
https://soundcloud.com...
Last seen:
3 days, 11 hours ago
Joined:
2 years, 9 months ago
Email:
j**********@gmail.com

Posts by O.rka

<prev • 108 results • page 1 of 11 • next >
0
votes
0
answers
143
views
0
answers
Comment: C: How to calculate percent identity from sam file?
... Nice, I didn't know you could do that! So you're suggesting for eukaryotic organisms with lots of splice sites to map directly to transcript, then filter with samtools view regions? ...
written 3 days ago by O.rka80
0
votes
0
answers
143
views
0
answers
Comment: C: How to calculate percent identity from sam file?
... Yea BBMap is definitely my go for 99% of my mapping jobs mostly because of this feature (and it's super fast, easy to use, and reliable). One thing about BBMap is it can't take in GTF/GFF3 files for exon mapping like HISAT2 & STAR. ...
written 3 days ago by O.rka80
0
votes
0
answers
143
views
0
answers
Comment: C: How to calculate percent identity from sam file?
... This pipeline I use relies on CLC mapper which has a percent identity parameter. It seems really useful and I want to make a public version that only uses open source tools so I can throw it on my GitHub. I want to make it so you can use any mapping program and then you can filter out the reads th ...
written 4 days ago by O.rka80
0
votes
0
answers
143
views
0
answers
Comment: C: How to calculate percent identity from sam file?
... How should indels be handled? ...
written 4 days ago by O.rka80
0
votes
0
answers
143
views
0
answers
Comment: C: How to calculate percent identity from sam file?
... I've changed the question to how to calculate from sam file. Is there a straight forward way to do this from the sam record? ...
written 4 days ago by O.rka80
3
votes
0
answers
143
views
5 follow
0
answers
How to calculate percent identity from sam file?
... I'm using `pysam` to calculate the percent identity from each mapped read in a samfile. I tried to get some of the more complicated CIGAR strings so I did `len(CIGAR) > 4`. I can't figure out how to calculate the percent identity from this. It would make sense to get the number of matches - th ...
assembly sam samtools mapping cigar written 4 days ago by O.rka80
0
votes
0
answers
47
views
0
answers
Are there any tools that can create a very basic GTF file from contig sequences (no annotations really needed) ?
... I want to use [featureCounts](http://bioinf.wehi.edu.au/featureCounts/) but it requires a GTF file. I really like the following two parameters for minimum percent identity and minimum spatial coverage (I think that's what these are below?) > --fracOverlap Minimum fraction of overlapping base ...
assembly mapping written 5 days ago by O.rka80
0
votes
0
answers
70
views
0
answers
Is there a tool that filters a sam/bam file by the following: (1) similarity score; (2) length fraction?
... I want to make a pipeline that can take sam files from different aligners like HISAT2. One thing I like about HISAT2 is you can either map the reads to a transcripts or a GTF file if you had one available. What I like about BBMAP is that it has `minid`: > minid=0.76 Approximate m ...
alignment next-gen rna-seq sequencing written 9 days ago by O.rka80
0
votes
0
answers
72
views
0
answers
Is there a tool that can identify frame shifted proteins from an assembly?
... I have a bunch of orthologs for a protein that has a native frame shift from the genomic dna. I’m looking for this protein in another organism. Is it possible to build an hmm from the final product proteins and then identify if it exists within a query dna while considering the frame shift aspect? ...
software error genome rna-seq written 10 days ago by O.rka80
6
votes
1
answer
156
views
6 follow
1
answer
Is there any benefit in sorting a sam/bam file by coordinates vs. queryname?
... I'm running the dropseq pipeline and there is a part where the samfile gets sorted. It looks like there is an option to either sort by coordinates or by queryname. Is there a benefit to either of these? ...
alignment written 12 days ago by O.rka80 • updated 12 days ago by h.mon24k

Latest awards to O.rka

Centurion 9 days ago, created 100 posts.
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Popular Question 3 months ago, created a question with more than 1,000 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 Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Scholar 5 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 7 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Popular Question 7 months ago, created a question with more than 1,000 views. For Most up-to-date Gene Ontology [GO] analysis?
Great Question 10 months ago, created a question with more than 5,000 views. For How to tell bloodtype from SNPs data?
Popular Question 11 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Popular Question 16 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Supporter 24 months ago, voted at least 25 times.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to tell bloodtype from SNPs data?
Student 2.6 years ago, asked a question with at least 3 up-votes. For Most up-to-date Gene Ontology [GO] analysis?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 984 users visited in the last hour