User: harish

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harish140
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Posts by harish

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Alternative to BLASR ?
... You can use pbindex to generate the index files. ...
written 4 weeks ago by harish140
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Comment: C: Enhancing draft genome using 10X data
... > Does anybody know any tool getting a draft genome and 10X reads and make the total size of the genome longer, not only making bigger scaffolds? If you have adequate coverage of 10X reads, get an assembly from SuperNova, chances are that it'll be more contiguous anyways. Otherwise, in order to ...
written 5 weeks ago by harish140
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Comment: C: Alternative to BLASR ?
... Minimap doesn't really care for fastq files tbh. As such the Sequel runs have series of '!!!!!!' representing the qualities anyways. You can definitely use Minimap's "-a" parameter to get a sam file and then convert it into Arrow specific format using pbbamify. Also take a look at pbbioconda repo ...
written 5 weeks ago by harish140
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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 3 months ago by harish140
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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 3 months ago by harish140
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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 3 months ago by harish140
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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 4 months ago by harish140
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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 4 months ago by harish140
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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 4 months ago by harish140
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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 4 months ago by harish140

Latest awards to harish

Scholar 4 months 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 5 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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