User: harish

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harish150
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Posts by harish

<prev • 36 results • page 1 of 4 • next >
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Answer: A: merging 10X genomics assemblies
... Why not try something like Meta-assembler/GARM etc? But generally speaking it's not advisable to merge scaffold level assemblies or assemblies hosting ambiguities. The ambiguities get propagated in a compounding fashion and may cause issues downstream. ...
written 2 days ago by harish150
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Comment: C: Enhancing draft genome using 10X data
... Ahh, no worries :) I know the pain of doing this time and time again :) Besides that's half the reason I asked you to run scaff10x. Arcs doesn't really seem to behave well in my hands :( ...
written 2 days ago by harish150
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Comment: C: Extract fasta-headers that have the same word
... That's a valid option, but sometimes fasta sequences might be wrapped in which case it might be a bit difficult. Why not use grep and parse it using a fasta parser? ...
written 7 days ago by harish150
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Comment: A: How to systematically check if a bam file is truncated
... samtools index should throw an error in case the file is truncated. ...
written 6 weeks ago by harish150
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Comment: C: Alternative to BLASR ?
... You can use pbindex to generate the index files. ...
written 3 months ago by harish150
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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 3 months ago by harish150
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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 3 months ago by harish150
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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 4 months ago by harish150
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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 5 months ago by harish150
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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 5 months ago by harish150

Latest awards to harish

Scholar 6 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 7 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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