User: pbigbig

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pbigbig170
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Posts by pbigbig

<prev • 82 results • page 1 of 9 • next >
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Answer: A: How to run Interproscan on cluster ?
... Hi, I suggest that you download the binary files of sfld from here: ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/bin/ then replace all files in ${INTERPROSCAN5HOME}/bin/sfld/ with them, it worked for me. ...
written 5 weeks ago by pbigbig170
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Comment: C: Transcriptomes comparison and check for shared transcripts with arbitrary simila
... Thanks for your suggestion, I will BLAT them to each other. Sorry for my clumsy explanation, for short, I just have RNAseq data from different individuals (same tissue and species), some of them are pretty small sized compared to others after deduplicate (because of PCR artifacts), therefore I would ...
written 8 weeks ago by pbigbig170
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Transcriptomes comparison and check for shared transcripts with arbitrary similarity
... Hi everyone, I have Illumina RNAseq data from individuals of 2 groups (2 different phenotypes), after preprocessing reads and running de novo assembly with Trinity, I have group 1st with assemblies sized from 45-55 Mb (megabyte, fasta format) and another group (group 2nd) with assemblies sized from ...
rnaseq de novo assembly transcriptome written 3 months ago by pbigbig170
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Comment: C: Confusion regarding Trinity analyze_diff_expr.pl
... thank you for your suggestion ! ...
written 5 months ago by pbigbig170
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(Closed) Confusion regarding Trinity analyze_diff_expr.pl
... Hi all, I have some confusion regarding 2 ways of usage of `analyze_diff_expr.pl` script in Trinity package. 1. In the usage instruction resides within script, we have to input matrix file: `${name}.TMM.EXPR.matrix` , as in: > # Required: > # > # --matrix TMM.EXPR. ...
trinity differential expression transcriptome written 5 months ago by pbigbig170
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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 5 months ago by pbigbig170 • updated 5 months 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 5 months ago by pbigbig170
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Comment: C: GC content calculation
... Thanks for your suggestion, I would check the code to be sure ...
written 5 months ago by pbigbig170
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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 5 months ago by pbigbig170
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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 5 months ago by pbigbig170 • updated 5 months ago by Brian Bushnell11k

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Popular Question 6 weeks ago, created a question with more than 1,000 views. For Jellyfish -C option explanation
Great Question 3 months ago, created a question with more than 5,000 views. For Run multiple fastq.gz files with FastQC and yield single report?
Popular Question 4 months ago, created a question with more than 1,000 views. For Jellyfish -C option explanation
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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Popular Question 16 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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