User: popayekid55

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popayekid5540
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Posts by popayekid55

<prev • 41 results • page 1 of 5 • next >
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Comment: C: Busco result interpretation
... Any other approach you opted to address the concern?? ...
written 3 months ago by popayekid5540
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Busco result interpretation
... Dear all, I have assembled a algal genome n predicted ~9k genes using Augustus. Genes were evaluated using Busco. Only 132 genes were put under different category of Busco (C,S,D,F and M). When I checked for *C reinhardtii*, around 300 genes were put under those categories. But in article they are ...
genome gene tool written 3 months ago by popayekid5540 • updated 3 months ago by charles.bridges60
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Comment: C: MSA of very long sequences?
... you could try using [mafft][1] [1]: https://mafft.cbrc.jp/alignment/software/ ...
written 4 months ago by popayekid5540
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Comment: C: Global symbol requires explicit package name issue
... Either remove the `use strict` from the code or use declare `$temp_seqid` as `my $temp_seqid. `use strict` enforces explicit defining the variables before use them ...
written 5 months ago by popayekid5540
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Comment: C: Gene type identification
... Thank you @genomax. i tried, it is only giving whether a gene is protein coding or other gene type. requirement is if it a protein coding what it is like an enzyme/tf/membrane protein etc. Could you please provide exact link if so. ...
written 5 months ago by popayekid5540
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Comment: C: Trinity de novo assembly without reference genome (community metatranscriptome)
... Can you share the pipeline?? I am about to start a metatranscriptome . Thank you ...
written 5 months ago by popayekid5540
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Gene type identification
... Hello all, I have set of gene symbols (ex Akt1, Brca1 etc) from mouse genome. Where can I find gene type based on what it encodes. Like is it a transcription regulator/ enzyme/ transmembrane protein/growth factor etc Thank you all ...
gene function database written 5 months ago by popayekid5540
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Comment: C: best kmer for genome size estimation
... Thank you for the response. I was following the [1st link][1] for genome estimation. It was mentioned for eukaryote 17-31 would be fine in jellyfish. In the tutorial they chose 25. Still not understanding how to choose the kmer length for counting. `kmercountexact.sh` is taking kmer length of 31 as ...
written 6 months ago by popayekid5540
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Comment: C: best kmer for genome size estimation
... I have tried that and best kmer from kmergenie was way too high. For this data it was 119. I was not sure this kmer to use in jellyfish for genome estimation ...
written 6 months ago by popayekid5540
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best kmer for genome size estimation
... Hi, How do i select a best kmer for genome size estimation using jellyfish. I did using 31 and 41 both gave me a different result. Read chemistry is 150*2. are there any other tools, i am trying [gce][1] also. Thanks in advance [1]: ftp://ftp.genomics.org.cn/pub/gce ...
genome kmer written 6 months ago by popayekid5540

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Supporter 22 months ago, voted at least 25 times.

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