User: harish

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harish200
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Posts by harish

<prev • 49 results • page 1 of 5 • next >
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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 8 weeks ago by harish200
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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 9 weeks ago by harish200
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Comment: C: Kronagram from Kraken2 output?
... Glad to know that it worked! ...
written 9 weeks ago by harish200
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Answer: A: Using 10X Chromium linked reads for genome gap-filling
... I don't think there would be dedicated tool for it, but essentially all gapfillers do is just map the reads, compute the consensus and patch the gaps up assuming adequate unique flanking regions are obtained. Since 10X reads are nothing but standard paired end libraries with 10X barcodes embedded, ...
written 9 weeks ago by harish200
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Comment: A: Kronagram from Kraken2 output?
... Possible duplicate of https://www.biostars.org/p/238858/ ? ...
written 9 weeks ago by harish200
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Comment: C: Genome assembly contig ordering
... You can scaffold them using many tools like BESST, SSPACE etc. However, ideally it wouldn't matter how you order the contigs (method), as there are many methods available. Does your organism have a closely related species preferably in chromosome? If yes, then you can RaGOO. ...
written 9 weeks ago by harish200
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Answer: A: Assembler for only nanopore data
... You can try Canu, Flye, Necat, Minimap-miniasm, Ra etc. ...
written 3 months ago by harish200
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Comment: C: Enhancing draft genome using 10X data
... Alright, can you link what version of Scaff10X you are using? There has been a newer one since the past few days. The recent one seems to fix a couple of issues, but I haven't had the opportunity to try, so I can't really comment on it. The following are the couple of steps that I generally follow: ...
written 3 months ago by harish200
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Answer: A: inputs to genomicconsensus arrow algorithm
... Hi, Why not slice the bam files to submit each contig as it's own reference to run arrow? After this you can merge back the genome fasta. ...
written 3 months ago by harish200
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Comment: C: Can I use two restriction enzymes to analyze HiC data using HiCExplorer
... Ahh, the latest update does support the ^N sites, I found about it on github. However you will definitely need to process your files in a compatible format if you are using Juicer etc. ...
written 3 months ago by harish200

Latest awards to harish

Scholar 10 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 11 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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