User: kumars.sv

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kumars.sv0
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Posts by kumars.sv

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Comment: C: RNAseq data analysis help
... a) From a different run (experiment), not from different lane, that too, a different experiment conducted on a different date (i.e control is sequenced on day 1 and samples are sequenced on day 62). Libraries are made on different days, not on the same day. b) Since there are no replicates per gro ...
written 8 weeks ago by kumars.sv0
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RNAseq data analysis help
... Hi all! Here is my question and your input is well appreciated. Experiment has 3 groups and each group has only one sample. Three groups are control, treated 1, treated 2. Treated 1 and Treated 2 have library size of 18 and 20 million reads respectively. Control has a library size of 70 million rea ...
batch-effect rna-seq library-size written 8 weeks ago by kumars.sv0
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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 11 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 11 months ago by kumars.sv0 • updated 11 months ago by WouterDeCoster42k
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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 12 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 12 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 12 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 12 months ago by kumars.sv0 • updated 12 months ago by h.mon28k

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