User: ashokkumar.mb

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Posts by ashokkumar.mb

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Forum: How to know that our trinity denovo assembly is good or not?
... I have used Trinity 2.8.4 to do denovo assembly of my plant RNA seq data. Now I have finished assembly, but how to know that this denovo assembly is really good and what are all the stats I should consider? N50 value is 2865 Total trinity 'genes':72392 Total trinity transcripts: 146848 ...
assembly forum written 11 weeks ago by ashokkumar.mb0 • updated 11 weeks ago by biokoala3.6k
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problem with updating trinity
... hi I have installed trinity v2.6 through conda. but whenever I try to update to trinityv2.8 through conda it says All requested packages already installed its not getting updated to v2.8. I have used `conda update trinity` command to update this. Is there any other way to do this? Please ...
software error tool written 12 weeks ago by ashokkumar.mb0 • updated 12 weeks ago by biokoala3.6k
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Comment: C: Need help to resolve trinity error
... Thank you so much Now its working ...
written 12 weeks ago by ashokkumar.mb0
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Comment: C: Need help to resolve trinity error
... Thank you so much Now its working ...
written 12 weeks ago by ashokkumar.mb0
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Need help to resolve trinity error
... I got this error message while trying to trinity Tuesday, November 20, 2018: 18:32:08 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /home/genetics/miniconda3/opt/trinity-2.6.6/util/support_scripts/ExitTester.jar 0 Tuesday, November 20, 2018: 18:32:08 CMD: java -Xmx64m -XX:ParallelGCThrea ...
assembly written 3 months ago by ashokkumar.mb0 • updated 3 months ago by RamRS20k
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Comment: C: Need help to do single denovo assembly with multiple RNA seq data
... Hey thank you so much, Found command for that ...
written 3 months ago by ashokkumar.mb0
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Need help to do single denovo assembly with multiple RNA seq data
... I have illumina RNA seq data from different tissues of one plant. Is it possible to do single assembly using all this RNA seq data from different tissues of one plant? Do I need to combine this libraries before assembly or is there any option in assembly tools itself? Thank you ...
assembly rna-seq written 3 months ago by ashokkumar.mb0 • updated 3 months ago by kristoffer.vittingseerup1.4k
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Comment: C: Need help to separate a genome in different x coverage
... Thank you so much for your help ...
written 3 months ago by ashokkumar.mb0
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Comment: C: Need help to separate a genome in different x coverage
... Thank you so much Yes, I would like to do downsample our genome coverage. I read BBTools guide and found a command to do downsample "bbnorm.sh in=reads.fq out=normalized.fq target=100 min=5". Do I need to concern about any other parameters in this? or Do I need to do use any other tool to downsampl ...
written 3 months ago by ashokkumar.mb0
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Need help to separate a genome in different x coverage
... We are developing a pipeline to identify plant SNPs and Structural variations. As a part of checking, we have to separate a plant genome in different X coverage. For instance, actual genome data coverage is 40 X, now we need to generate it in different X coverage like 10X, 20x and 30x. Is it possibl ...
x coverage plant genome normalization written 3 months ago by ashokkumar.mb0 • updated 3 months ago by Vitis1.9k

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