User: ever_wudi

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ever_wudi10
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Posts by ever_wudi

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Comment: C: Generating FPKM matrix accross all samples after stringtie
... I see, thank you very much! ...
written 11 months ago by ever_wudi10
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Answer: A: Outputing gexpr() with gene_name (or gene symbol) instead of MSTRG.x gene_id
... I figured out one way to do it. I used whole_tx_table = texpr(my.humandata, 'all') to extract everything into whole_tx_table then do final_fpkm_table = whole_tx_table[c("gene_name","sample 1","sample 2", ..)] to slice out only the gene_name and fpkm values, then write final_fpkm_table to a .cvs ta ...
written 11 months ago by ever_wudi10
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Comment: C: Generating FPKM matrix accross all samples after stringtie
... Thanks for the tips. What are the better metrics used now? TPM or some others? ...
written 11 months ago by ever_wudi10
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Comment: C: Generating FPKM matrix accross all samples after stringtie
... Hi ATpoint, I have another question. When I use gexpr() to output the matrix, it generates a matrix with MSTRG.x gene ids as identifiers. However, I really need gene_name (or gene symbol) as my gene identifiers for the next step. I tried really hard to fiddle it around and search online but still ca ...
written 11 months ago by ever_wudi10
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Outputing gexpr() with gene_name (or gene symbol) instead of MSTRG.x gene_id
... Hi, I am trying to use Ballgown to output gene-sample expression matrix. What I did is `geneexp = gexpr(bg)`, then `write.csv(geneexp, "output.csv", row.names = TRUE)`. However, I could only get it output matrix with MSTRG.x gene ids as identifiers. How can I output the matrix with gene_name (or gen ...
ballgown stringtie rna-seq gene_name written 11 months ago by ever_wudi10
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Comment: C: Generating FPKM matrix accross all samples after stringtie
... Thanks for reminding. I didn't intend to feed the count matrix to EdgeR or DESeq2, so I just needed the matrix in the FPKM form. Is there something wrong with the FPKM normalization method? ...
written 11 months ago by ever_wudi10
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Comment: C: Generating FPKM matrix accross all samples after stringtie
... I just saw this message, and just realized there is a "tick" sign for marking an accepted answer. I already marked it accepted. ...
written 11 months ago by ever_wudi10
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Comment: C: Transformed cancer cell-lines RNA-seq database
... This can be a very useful site and your suggested way makes sense. Thanks a lot, jared.andrews07 (thumb up)! ...
written 11 months ago by ever_wudi10
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Transformed cancer cell-lines RNA-seq database
... Hi, I am trying to find a database which has RNA-seq data for cancer cell-lines transformed from normal cells by specific oncogenes or mutated tumor suppressors. I'm not looking for RNA-seq on patient cells (like in TCGA) because they contain many other mutations so the cancer formation is hard to ...
genome rna-seq written 11 months ago by ever_wudi10 • updated 11 months ago by jared.andrews072.7k
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Comment: C: Generating FPKM matrix accross all samples after stringtie
... Thanks ATpoint, the commands worked. I am very new to R and RNA-seq, did try to search for solutions before but didn't find a satisfactory way. Thanks for the help. ...
written 12 months ago by ever_wudi10

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