User: gozrom

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gozrom80
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Posts by gozrom

<prev • 17 results • page 1 of 2 • next >
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Comment: C: TPM from StringTie
... Figured the error when I substitute the FUN argument to any of a functional definition it works, but it only aggregate gene names without showing TPM values... I need both I need the sum of all the TPM values from all the transcripts specific to each gene, and also the gene list ...
written 2.1 years ago by gozrom80
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Comment: C: TPM from StringTie
... Thanks, that seems simpler than what I wrote, I tried aggregate but got an error: Error in match.fun(FUN) : 'length(genes_list$ref_gene_name)' is not a function, character or symbol If I run length(genes_list$ref_gene_name) as is it gives me the length of the specific column. but when I do it ...
written 2.1 years ago by gozrom80
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Comment: C: RSEM on single replicate with multiple fasta files
... Thanks, that seems to work... ...
written 2.1 years ago by gozrom80
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RSEM on single replicate with multiple fasta files
... Hi, there, I'm running RSEM on 12 replicates each replicate has 8 fasta files, paired-end reads. This is inside 2 For loops with i from 1 to 4 and j from 1 to 4 rsem-calculate-expression -p 8 --bowtie2 --paired-end --strandedness forward --append-names --estimate-rspd --output-genome-bam ~/R ...
rna-seq written 2.1 years ago by gozrom80
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Comment: C: How to avoid MSTRG from StringTie
... I did use this option like it's been described in Pertea 2016 Hisat Stringtie ballgown paper. MSTRG are still there.... ...
written 2.2 years ago by gozrom80
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Comment: C: How to avoid MSTRG from StringTie
... I used this one: ftp://ftp.ensembl.org/pub/release-91/gtf/mus_musculus/Mus_musculus.GRCm38.91.gtf.gz You suggest that this is not good enough? ...
written 2.2 years ago by gozrom80
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TPM from StringTie
... I have extracted all the TPM values from gtf files generated by StringTie for all replicates, however Those TPM values are per transcript and not per gene. Now I have one huge csv file with 12 replicates and their corresponding TPM values and I want to make the TPM values per gene to use it in a su ...
rna-seq written 2.2 years ago by gozrom80 • updated 12 months ago by ATpoint34k
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How to avoid MSTRG from StringTie
... Hi, there, I've used Hisat-StringTie-ballgown pipeline and Using mouse genome 91 gtf file from ensemble creates MSTRG values as partial output of Stringtie, The number of those MSTRG can be high, and I'm not sure is a real, as too many new transcripts, or unassembled transcripts. Is there a diff ...
rna-seq written 2.2 years ago by gozrom80
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Comment: C: Stringtie to DESeq2
... @Kevin Great it works. Thank you ...
written 2.2 years ago by gozrom80
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Comment: C: Stringtie to DESeq2
... @Kevin Blighe, that seem to work with python 2.7, I have other issue, that it doesn't see gtf file, I'll try troubleshooting it myself first, Thanks for the help. ...
written 2.2 years ago by gozrom80

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