User: shivyasoni1994

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Posts by shivyasoni1994

<prev • 15 results • page 1 of 2 • next >
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Histogram of p values for all tests
... Hi, I am trying to do differential-gene-expression analysis with DESeq2, for that i have done pseudo-alignment using Salmon , and with tximport, gene-level abundance is calculated. I am following "Analyzing RNA-seq data with DESeq2", tutorial. I got Histogram of p values for all tests. ![enter imag ...
deseq2 rna-seq written 4 months ago by shivyasoni19940 • updated 4 months ago by tw61720
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Comment: C: Salmon (error: SAM file and fasta file have different transcript length)
... Thanks !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ...
written 4 months ago by shivyasoni19940
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Comment: C: unable to load quant.sf files
... Thankyou so much, it solved my problem.. thankyou!!!! ...
written 5 months ago by shivyasoni19940
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Comment: C: unable to load quant.sf files
... Thankyou ......................! ...
written 5 months ago by shivyasoni19940
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unable to load quant.sf files
... Hi, I am am trying to use tximport, but running into: all(file.exists(files)) [1] FALSE I started like this: I imported the libraries library("tximport") then library("readr") I refered to directory, containig the quant.sf files dir <- '/home/dell/Desktop/quant' in ...
tximport R written 5 months ago by shivyasoni19940
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Comment: C: Salmon (error: SAM file and fasta file have different transcript length)
... Hi Rob, what does -g [ --geneMap ] do?? If this flag is passed, then tximport is no more required?? which is used to input quant.sf in DESeq2?? ...
written 5 months ago by shivyasoni19940
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Comment: C: Salmon (error: SAM file and fasta file have different transcript length)
... Thanks Rob !!!!!!!!!!!!!! :) ...
written 5 months ago by shivyasoni19940
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Comment: C: Salmon (error: SAM file and fasta file have different transcript length)
... Thanks a lot, this explanation is very helpful!! Should I go for quasi-mapping-based mode or FMD-index-based mode, as I want to go for , Differential-gene-expression analysis. ...
written 5 months ago by shivyasoni19940
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Comment: C: Salmon (error: SAM file and fasta file have different transcript length)
... Thanks for explaining, in such easy manner, I actually aligned against coding-sequences(CDS), as aligning with genome requires high computational memory. > This brings me to my last question / suggestion. Is there a specific > reason you want to run salmon in alignment-based mode? I want to ...
written 5 months ago by shivyasoni19940
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Comment: C: Salmon (error: SAM file and fasta file have different transcript length)
... Thanks for reply, The portion of GTF file, containing, transcript_id: ENST00000618686.1, looks like this, GL000009.2 ENSEMBL transcript 56140 58376 . - . gene_id "ENSG00000278704.1"; transcript_id "ENST00000618686.1"; gene_type "protein_coding"; gene_name "BX004987.1"; transcript_type "protein_c ...
written 5 months ago by shivyasoni19940

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