User: pbigbig

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pbigbig160
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Posts by pbigbig

<prev • 80 results • page 1 of 8 • next >
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Transcriptomes comparison and check for shared transcripts with arbitrary similarity
... Hi everyone, I have Illumina RNAseq data from individuals of 2 groups (2 different phenotypes), after preprocessing reads and running de novo assembly with Trinity, I have group 1st with assemblies sized from 45-55 Mb (megabyte, fasta format) and another group (group 2nd) with assemblies sized from ...
rnaseq de novo assembly transcriptome written 29 days ago by pbigbig160
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Comment: C: Confusion regarding Trinity analyze_diff_expr.pl
... thank you for your suggestion ! ...
written 12 weeks ago by pbigbig160
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(Closed) Confusion regarding Trinity analyze_diff_expr.pl
... Hi all, I have some confusion regarding 2 ways of usage of `analyze_diff_expr.pl` script in Trinity package. 1. In the usage instruction resides within script, we have to input matrix file: `${name}.TMM.EXPR.matrix` , as in: > # Required: > # > # --matrix TMM.EXPR. ...
trinity differential expression transcriptome written 3 months ago by pbigbig160
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Confusion regarding Trinity analyze_diff_expr.pl
... Hi everyone, I have some confusion regarding two ways of usage of `analyze_diff_expr.pl` script in the Trinity package. In the usage instruction resides within script, we have to input matrix file: `${name}.TMM.EXPR.matrix` , as following: > # Required: > # > # --matrix ...
trinity differential expression transcriptome written 3 months ago by pbigbig160 • updated 12 weeks ago by Farbod2.9k
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Comment: C: GC content calculation
... Thanks, It is really a tie-breaker, here's what I have got: A C G T N IUPAC Other GC GC_stdev 0.2773 0.2281 0.2383 0.2563 0.0000 0.0000 0.0000 0.4664 0.0675 ...
written 3 months ago by pbigbig160
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Comment: C: GC content calculation
... Thanks for your suggestion, I would check the code to be sure ...
written 3 months ago by pbigbig160
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Comment: C: GC content calculation
... Thanks, It doesn't contain U, below is the full output of TrinityStats, I think it based on all contigs for GC content calculation: Counts of transcripts, etc. Total trinity 'genes': 68518 Total trinity transcripts: 72229 Percent GC: 46.64 Stats based on ALL transcript con ...
written 3 months ago by pbigbig160
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GC content calculation
... Hi everyone, I have some confused results regarding GC content in transcriptome, I have made a transcriptome de novo assembly by Trinity, and exploited some prebuild scripts (i.e TrinityStats) in Trinity package to calculate basic statistics of assembled transcriptome, it returned **GC% = 46.64 %.* ...
trinity gc content transcriptome written 3 months ago by pbigbig160 • updated 3 months ago by Brian Bushnell10k
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Comment: C: Gene Set Enrichment Analisys on Bioconductor?
... I just have a small question, how big is your gene set, because 3000 unique genes is huge for analyzing, the number of functional clusters is hundreds and it is difficult to infer meaning from them. ...
written 4 months ago by pbigbig160
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Comment: C: Tools for categorize COG/KOG list
... Thank you very much for your suggestion ! ...
written 5 months ago by pbigbig160

Latest awards to pbigbig

Great Question 5 weeks ago, created a question with more than 5,000 views. For Run multiple fastq.gz files with FastQC and yield single report?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Jellyfish -C option explanation
Popular Question 9 weeks ago, created a question with more than 1,000 views. For kmergenie can not execute on a file because directory not exist?
Popular Question 4 months ago, created a question with more than 1,000 views. For kmergenie can not execute on a file because directory not exist?
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Student 9 months ago, asked a question with at least 3 up-votes. For Run multiple fastq.gz files with FastQC and yield single report?
Popular Question 14 months ago, created a question with more than 1,000 views. For Run multiple fastq.gz files with FastQC and yield single report?

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