User: kumars.sv

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kumars.sv0
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Posts by kumars.sv

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Comment: C: Feedback requested for pooling biological samples for NGS
... We send the samples to commercial providers. 3 samples without pooling are charged for 3 samples. Same problem as biotech deepti from https://www.biostars.org/p/202139/#202192 and kumar issue from https://www.biostars.org/p/157946/#157964. Commercial vendors promise statistical significance and di ...
written 8 months ago by kumars.sv0
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Feedback requested for pooling biological samples for NGS
... Hi all, I have a question regarding NGS experiment set-up and sample pooling. We are currently planning WES and RNAseq of human samples between normal and tumor groups. We will also confirm the same in cell lines. Experimental setup suggested by PI is to pool 3 replicates in to one sample per group ...
sample pooling next-gen sequencing written 8 months ago by kumars.sv0 • updated 8 months ago by WouterDeCoster40k
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Comment: C: Calculating alignment/mapping time
... Well, that question got downvoted and hmon suggested to move the query to bioinformatics.stackexchange. Moved it bioinformatics stack exchange. ty hmon ...
written 9 months ago by kumars.sv0
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Comment: C: Calculating alignment/mapping time
... I understand that it is tricky to calculate the estimated time for assembly and there are several factors that influence the assembly. It seems there is no such tool. For your PS point, what would be the suggested assembler, in terms of memory management and resources for polyploid genomes? Btw, th ...
written 9 months ago by kumars.sv0
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Comment: C: Calculating alignment/mapping time
... Since there was no reply, I have reposted this on SO here: https://stackoverflow.com/questions/53314743/calculating-alignment-mapping-time ...
written 9 months ago by kumars.sv0
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Calculating alignment/mapping time
... I am trying to assemble a plant genome using AWS resources using velvet. Plant genome is huge (> 10 times human genome) and coverage is around 30 x. We are planning for *de novo* assembly with Velvet (threads enabled). I would like to know if there is a calculator that can provide approximate tim ...
calculation ngs mapping velvet denovo assembly written 9 months ago by kumars.sv0 • updated 9 months ago by h.mon27k

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