User: harish

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harish130
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Posts by harish

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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 3 days 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 3 days 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 4 days 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 17 days 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 19 days 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 20 days 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 25 days ago by harish130
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Answer: A: Gene ontology analysis
... Generally speaking, you can call these over-representation tests. You can represent these as a Scatter-plot (dot-plot) as well, ordered on the basis of p/qvalues and ratio of genes in your study in that pathway over the number of total genes in that pathway. See reference image under dotplot sectio ...
written 25 days ago by harish130
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Answer: A: Assessing The Quality Of De Novo Assembled Data
... Also a couple of other parameters to judge on are: 1. Mapping of a closer species or your own RNAseq data. 2. Duplicated contigs in your assembly. I have seen this in case of multiple genome where the unique genomic content is very low. 3. If you can predict ORFs, then one of the better approach ...
written 27 days ago by harish130
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Answer: A: Using RNA-seq reads from closely related species in BRAKER2 genome annotation pi
... It depends. The following questions have to be answered by you. Are the organisms in the same family or genus? How is the alignment rate? How much can you compromise on the false-positives? Generally if the species are in the same genus or family, then it is generally fine for you to use those d ...
written 28 days ago by harish130

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Teacher 8 weeks 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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