User: T_18

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T_1820
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Posts by T_18

<prev • 26 results • page 1 of 3 • next >
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Trimmomatic confirmation, multiple indeces per sample?!
... Hi! I received my HiSeq Illumina RNAseq data and want to run trimmomatic to remove bad quality reads and trim adapters. I have used trimmomatic before but I am currently in doubt if I create the adapter file in a correct way given the fact that I received multiple indeces per sample, can someone pl ...
trimmomatic rnaseq trimming written 1 day ago by T_1820 • updated 1 day ago by finswimmer8.0k
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Comment: C: Puzzled by GOseq analyses
... Yes, it's RNAseq data. I'm currently home, but will provide the code when I'll be in the office tomorrow. Thanks so far. ...
written 3 months ago by T_1820
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Puzzled by GOseq analyses
... Dear all, I am currently trying to run a GO enrichment analysis using GOseq but I am slightly puzzled if I am doing things correctly given my (zero) output. My endgoal is to get results I can use in GOgadget. I have the following files: - Factor labels (either differently expressed or not, so two ...
R gogadget goseq written 3 months ago by T_1820
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Comment: C: Binning GO terms into broader (more usefull) GO terms
... This seems indeed exactly what I was looking for! I'm currently following the analysis steps, but I am stuck. (That is not part of this question so do not want to put that here). ...
written 3 months ago by T_1820
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Comment: A: Binning GO terms into broader (more usefull) GO terms
... Thanks for your reply. To be precise about my goal: I have a list of 2500 differentially expressed annotated transcripts with GO terms. I think it is very usefull to split these 2500 genes into smaller chunks according to 'function' based on the GO terms. These can be relatively big like, developmen ...
written 3 months ago by T_1820
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Binning GO terms into broader (more usefull) GO terms
... Dear all, For quit some hours I have been looking for a way to bin a list of GO terms into broader, more functional, (GO term groups). More specific: I have a list of 100s of GO terms with quit specific information and I want to bin/group them into useful groups like: "development" and "metabolitio ...
go written 3 months ago by T_1820 • updated 3 months ago by b.nota5.4k
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(Closed) Removing text after pattern using sed
... Dear all, I am just new in the world of sed.. Simple question, but struggling now for quit a while with this: I have a list of gene names: CYP6k1 CYP4L15 CYP354A5 CYP4d8 CYP354A5 CYP354A14 CYP4c1 CYP354A5 CYP4V2 CYP354A5 I only want to keep "CYP" and the n ...
sed unix written 4 months ago by T_1820 • updated 4 months ago by genomax59k
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(Closed) export PATH= fails...!
... Dear all, To run the program MCSC I need to add the diamond binary file into my executable search path. The path to the program is "/media/biosys5/bigDisk/Users/Programs/diamond" So I tried: export PATH=$PATH:/media/biosys5/bigDisk/Users/Programs/diamond also: export PATH=/media/biosys5/bigDisk/ ...
command line mcsc diamond unix written 5 months ago by T_1820
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Comment: C: Python script to remove sequences from a fasta file
... I used the fix of goodez. Although reading the script of finswimmer must solve the issue also (but did not test). ...
written 5 months ago by T_1820
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Comment: C: Python script to remove sequences from a fasta file
... Done, thanks.. Never did this before. ...
written 5 months ago by T_1820

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