User: harish

gravatar for harish
harish320
Reputation:
320
Status:
Trusted
Location:
Last seen:
8 months, 1 week ago
Joined:
3 years, 2 months ago
Email:
h*****@nucleomeinfo.com

Posts by harish

<prev • 56 results • page 1 of 6 • next >
1
vote
2
answers
217
views
2
answers
Answer: A: Correlation between coverage and variant calling
... Also there are quite a few relevant blog posts from Brad Chapman about this on bcbio and a lovely article by Heng Li. Heng Li's article: https://academic.oup.com/bioinformatics/article/30/20/2843/2422145 Bcbio posts: https://bcbio.wordpress.com/2013/10/21/updated-comparison-of-variant-detection-me ...
written 9 months ago by harish320
1
vote
2
answers
274
views
2
answers
Answer: A: found non conserved regions between 2 genomes
... Why not use Orthofinder? Give a couple of files containing protein sequences for each species and let it work its magic through. ...
written 11 months ago by harish320
1
vote
4
answers
3.1k
views
4
answers
Answer: A: best kmer for genome size estimation
... I tend to use ntCard and then throw the histograms at genomescope; both of which can be run offline. You just need to modify the files a little bit. Remove the F* lines and change the separator to space instead of tab. There isn't any particular kmer that is golden. It will depend on your species ...
written 11 months ago by harish320
2
votes
1
answer
13k
views
1
answers
Answer: A: Polish PacBio assembly with latest PacBio tools : an affordable solution for eve
... PSA for any one browsing this thread, Arrow tools have been branded as gcpp if you are using their bioconda environment. For faster polishing you can also use the following approach: **1/ Align and sort using pbmm2:** pbmm2 align genome.fasta movie.subreads.bam aligned.movie.bam --sort -j 8 - ...
written 13 months ago by harish320
0
votes
1
answer
321
views
1
answers
Answer: A: Best tool for variant calling in polyploids
... Why not try Freebayes? It has an option to split up the variant calls to parallelize as well as account for polyploids. ...
written 13 months ago by harish320
0
votes
1
answer
318
views
1
answers
Comment: C: How to subset bamfile based on chromosome IDs
... Why not just use freebayes-parallel? Check this github thread: https://github.com/ekg/freebayes/issues/465 ...
written 13 months ago by harish320
1
vote
2
answers
1.3k
views
2
answers
Answer: A: VCF merge or concatenate?
... Bcftools does this, but is much faster than vcftools. You have one sample, but the data is split. You'll use a concatenation function., which is bcftools concat. However, if you have multiple samples, you'll want to merge them together, so use bcftools merge. In either of the cases, it wouldn't m ...
written 16 months ago by harish320
0
votes
2
answers
830
views
2
answers
Comment: A: Is it possible to use genomic reads from PacBio and Nanopore with Illumina RNA-s
... How much coverage on the Longer reads are you looking at? Also how much data do you have from RNASeq? It might just be easier to assemble the longer reads together and then use the RNASeq data to scaffold. ...
written 18 months ago by harish320
0
votes
1
answer
776
views
1
answers
Comment: C: Using 10X Chromium linked reads for genome gap-filling
... I don't know about the fidelity of what I'm about to suggest, but maybe breaking the scaffold sequences at a specific amount of "N"s and using these pseudo-contigs might probably help. ...
written 18 months ago by harish320
0
votes
1
answer
621
views
1
answers
Comment: C: Kronagram from Kraken2 output?
... Glad to know that it worked! ...
written 18 months ago by harish320

Latest awards to harish

Scholar 2.2 years ago, created an answer that has been accepted. For A: What is the next step after download the ncbi sra data of pacbio RSII sequencing
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: How to convert transcript level TPM to gene level TPM ?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1709 users visited in the last hour