User: Sitara

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Sitara0
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Posts by Sitara

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Maximum size limit for indexing genome with bowtie2 with large index option
... Thank you. Will look into it. ...
written 8 days ago by Sitara0
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Comment: C: Maximum size limit for indexing genome with bowtie2 with large index option
... It is a multiple genome fasta file ...
written 11 days ago by Sitara0
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Comment: C: Maximum size limit for indexing genome with bowtie2 with large index option
... I am running on a 256 gb RAM machine with 35 cores ...
written 11 days ago by Sitara0
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Maximum size limit for indexing genome with bowtie2 with large index option
... Hello all I have a fasta file with 100 GB of data and I am trying to create a bowtie2 index. It is showing the following error: Ran out of memory; automatically trying more memory-economical parameters. Using parameters --bmax 54 --dcv 4096 Any help would be appreciated. Thanks i ...
genome assembly alignment software error written 11 days ago by Sitara0 • updated 9 days ago by Biostar ♦♦ 20
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Comment: C: Selection of RNA-Seq appropriate tools for meta-analysis
... Thanks for your suggestion, will try to implement it. ...
written 3 months ago by Sitara0
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Selection of RNA-Seq appropriate tools for meta-analysis
... Hello all, I am running a meta-analysis with publicly available RNA-seq data, containing multiple samples which have approximately 5000 replicates each. I want to compare these samples and get the top genes which are up-regulated and down-regulated. Can someone suggest me Which combination of too ...
alignment rna-seq written 3 months ago by Sitara0 • updated 3 months ago by Devon Ryan84k
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Comment: C: RNA-Seq Cufflinks normalization methods
... This was clear enough for me to understand. Thanks a lot for the reply. ...
written 3 months ago by Sitara0
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Comment: C: RNA-Seq Cufflinks normalization methods
... Sorry. I am new to Biostar and I am learning things. Will use ADD COMMENT or ADD REPLY in the future. Could you please help me with the above query. Thank you. ...
written 3 months ago by Sitara0
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Comment: A: RNA-Seq Cufflinks normalization methods
... Thank you very much for the reply. Couldn't agree more here. I have stopped using TopHat2 or Cufflinks for the analysis. This is just a query, based on already analyzed data. All I want to know is, Cufflinks has classic FPKM as the normalization method CuffDiff has geometric normalization (default ...
written 3 months ago by Sitara0
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RNA-Seq Cufflinks normalization methods
... I used tudexo to analyze the samples of drosophila melanogaster. I used Tophat2 for alignment. There are differences in the results when used with different library normalization methods. So, I am not sure which library normalization is appropriate to use. And also will be thankful if I get to know ...
assembly rna-seq sequencing written 3 months ago by Sitara0 • updated 3 months ago by Devon Ryan84k

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