User: biologo

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biologo10
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Posts by biologo

<prev • 24 results • page 1 of 3 • next >
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how to judge the 10X genomics single cell data quality
... Dear all, i am analysis 10X genomics single cell data these days, but i donot know the specific standard to filter the sample, like how many gene it detect, how many cell it should have? or what other factors i should notice. Thanks for your help. ...
single cell written 23 days ago by biologo10
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Is that possible to draw the gene structure from bed file
... Hi, everyone, I have the bed file in such kind of format: ENSMUSG00000025925 15805904 15805932 cds ENSMUSG00000045216 36106069 36106094 utr3 ENSMUSG00000001138 36513045 36513067 cds ENSMUSG00000065629 39519551 395 ...
gene structure written 11 weeks ago by biologo10 • updated 11 weeks ago by jrj.healey4.6k
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trinity assembly error
... Dear friends: i was using trinity to do de novo assembly, since the data is very large, but the RAM and CPU ls limited, so it always occur like: (it do report the problem, but it still continue the work, i just wondering whether it will cause some problems for the result. do i need to stop it and r ...
rna-seq written 10 months ago by biologo10
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Comment: C: if i do mistake in library type parameter of trinity assembly, do i need to reas
... yes, i also considered that, but my colleague suggested me use ingap-cdg, have you ever use that, he told me it really works, and i also did the test, and only left 7,000,000 transcripts, seems good, but i am still doubt about the result. ...
written 11 months ago by biologo10
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Comment: C: if i do mistake in library type parameter of trinity assembly, do i need to reas
... accepted,but the thing is there's no reference genome for this species, and for some reasons, the genome assembly is really hard, to much AT ratio and repeat region, so, we just wanna focusing on the transcriptome assembly. thank you for your kind reply. ...
written 11 months ago by biologo10
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Comment: C: if i do mistake in library type parameter of trinity assembly, do i need to reas
... yes, i did. trim the adaptor and filter some short or low quality reads, but the trinity result seems no better options, thank you for your patience and your kind reply. ...
written 11 months ago by biologo10
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Comment: C: if i do mistake in library type parameter of trinity assembly, do i need to reas
... i got it, thank you, but your extral advice remind me that actually the quality is not good, even i isolate the llongest unigene, i got over 430,000 transcriptome. ...
written 11 months ago by biologo10
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if i do mistake in library type parameter of trinity assembly, do i need to reassemble it again?
... Dear friends, i was doing the trinity assembly, but i made a small mistake that for the --library type parameter, i used the FR, but actually it was RF, till i did the blast that i found the known gene matched to the reverse strand, cause the trinity take times and CPU, can i just reverse the Trini ...
assembly rna-seq written 11 months ago by biologo10 • updated 11 months ago by colindaven690
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repeatscout, run filter-stage-1.prl and get empty file
... hello everyone i m try to work with repeatscout but every time when i m runninf filter-stage-1.prl, the filtered library generated is created empty( no data)..... any solution??? ...
genome annotation written 13 months ago by biologo10
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Comment: C: Trinotate error DBD::SQLite::db do failed: no such table:
... yes, i find it for a long time, and thank you for your link ...
written 13 months ago by biologo10

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