User: tianshenbio

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tianshenbio40
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Posts by tianshenbio

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Comment: C: Gffread_How to obtain fasta files of gene features (ORF, UTR) by transcripts bas
... Thank you for your answer Juke34, will give it a try ...
written 21 hours ago by tianshenbio40
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Gffread_How to obtain fasta files of gene features (ORF, UTR) by transcripts based on gff?
... I have a gff like this: Bany_Scaf24 maker gene 41357 46444 . + . ID=Bany_09696;Name=Bany_09696;Alias=maker-Bany_Scaf24-exonerate_est2genome-gene-0.0; Bany_Scaf24 maker mRNA 41357 46444 . + . ID=Bany_09696-RA;Parent=Bany_09696;Name=Bany_09696-RA;Alias=maker-Bany ...
genome assembly sequence rna-seq gene written 22 hours ago by tianshenbio40
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Comment: C: After read mapping, count exons or genes?
... Ok now I understand, thank you. ...
written 1 day ago by tianshenbio40
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How to extract sequence of a specific feature in gff
... I have a gff file like this: Bany_Scaf24 maker gene 41357 46444 . + . ID=Bany_09696;Name=Bany_09696;Alias=maker-Bany_Scaf24-exonerate_est2genome-gene-0.0; Bany_Scaf24 maker mRNA 41357 46444 . + . ID=Bany_09696-RA;Parent=Bany_09696;Name=Bany_09696-RA;Alias=maker-Bany_Scaf24-exonerate_est2gen ...
genome assembly gff rna-seq written 1 day ago by tianshenbio40 • updated 1 day ago by Juke344.1k
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After read mapping, count exons or genes?
... I have mapped my RNA-seq reads (paired-end) onto the reference genome. Now I hope to measure the expression level by genes using featurecounts. Do I count the number of reads mapped to the whole 'gene' region, which includes introns? Or I should count reads mapped to all exons belonging to the same ...
genome featurecounts rna-seq written 1 day ago by tianshenbio40 • updated 1 day ago by ATpoint34k
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Comment: C: Many paralogous genes in GO enrichment results
... I am not sure how to do so...They have been annotated as distinct 'genes' in the gff file, no isoform tags, or anything I can use to distinguish them. The only thing I know is that they usually have adjacent ID numbers, and they are annotated with the same/similar gene names. Apparently I cant clus ...
written 2 days ago by tianshenbio40
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Comment: C: Many paralogous genes in GO enrichment results
... That's true... The problem is that I am working with a non-model organism. In the genome gff file I created, isoforms are annotated as distinct genes with distinct IDs...So I don' t know if I could pool them under the same gene...would be hard to do ...
written 2 days ago by tianshenbio40
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Many paralogous genes in GO enrichment results
... I performed a GO enrichment analysis for a list of DE genes. In the end, I got ~20 GO terms enriched. When I check the DE gene names under each GO term, it appears that almost all the genes have the same names or isoforms so it is reasonable that they have the same 'GO labels'...What I expect in a G ...
gene enrichment rna-seq go written 2 days ago by tianshenbio40
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How to generate a dataframe of deseq2 result excluding 'low counts' and 'outliers' ?
... In the following analysis using deseq2 dds_out <- DESeq(dds) res <- results(dds_out) summary(res) out of 19287 with nonzero total read count adjusted p-value < 0.1 LFC > 0 (up) : 3502, 18% LFC < 0 (down) : 4187, 22% outliers [1] : 0, 0% ...
deseq2 rna-seq written 6 days ago by tianshenbio40 • updated 5 days ago by Kevin Blighe59k
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Comment: C: What to choose as background genes in GO enrichment analysis
... Thank you for your answer! Very helpful ...
written 6 days ago by tianshenbio40

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