User: harish

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harish130
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Posts by harish

<prev • 29 results • page 1 of 3 • next >
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Answer: A: Protein categorization using COG
... Why not use eggNOG-mapper or look at NCBI's structure database [ here][1] [1]: https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi ...
written 21 days ago by harish130
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Answer: A: Is there no way to bypass the Windows requirement for working with Thermo RAW fi
... Not really a solution but don't these Tools work on Wine or Crossover? I do remember a buddy doing this long back, so I might be wrong. ...
written 4 weeks ago by harish130
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Comment: C: Issues with mapping reads onto Reference genome using bwa mem
... if you absolutely have to use nohup, use it this way: nohup sh -c 'bwa ......' This would initiate a shell for the command enclosed. The main error as another comment pointed out is that nohup is also redirecting stderr(?) to the sam file. ...
written 6 weeks ago by harish130
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Comment: C: Using RNA-seq reads from closely related species in BRAKER2 genome annotation pi
... For QC? I had used FastQC+Trimmomatic. I found it sufficiently fast and good enough, given I picking up reads with q30 or more only. I'm just using the RNAseq data to derive gene-structure hints to be honest, as I had a very good assembly (N50>7Mb, #Contigs/Scaffolds - 1300/900) with core gene s ...
written 7 weeks ago by harish130
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Comment: C: Using RNA-seq reads from closely related species in BRAKER2 genome annotation pi
... Yes, I do tend to do minimal QC on the reads like removing adapter, trimming low quality bases etc. But other than that, I tend to use all the reads that would have been QC'd. I haven't followed Khmer recipes, partly because I was able to setup other alternatives faster and mostly since I've been ...
written 7 weeks ago by harish130
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Answer: A: What is the next step after download the ncbi sra data of pacbio RSII sequencing
... Since you say that you are getting Fastq/fasta files, the first step is to correct them. The best way to go about it is to either use Falcon till the generation of preads or Canu's correct-trim mode or use proovread. If you had the bax/bam files, this would have been easier as you could import them ...
written 7 weeks ago by harish130
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Answer: A: Options for long-read diploid assembly
... You can created a smashed haplotype from Canu and later use WhatsHAP or similar approaches. But other than that IIRC, Falcon/Unzip is the only method. Also if you have parental samples, you can check trio-binning approach as well. ...
written 9 weeks ago by harish130
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Comment: C: Why learn programming in bioinformatics?
... GNU Datamash will save you eons of your time then! It's an amazing piece of work. ...
written 9 weeks ago by harish130
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Answer: A: Visualizing contig alignment
... If you have mummer alignments, you can probably use Circlize or AliTV. Alternatively, you can also use Gepard or minidot etc to view dot-plot alignments. ...
written 10 weeks ago by harish130
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Comment: C: How can I get only the rows when for the converge points : - +
... You can find lot's of examples and other tutorial's on [Grymoire][1]. [1]: http://www.grymoire.com/Unix/Awk.html ...
written 10 weeks ago by harish130

Latest awards to harish

Scholar 7 weeks 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 3 months ago, created an answer with at least 3 up-votes. For A: How to convert transcript level TPM to gene level TPM ?

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