User: Newbie

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Newbie0
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Posts by Newbie

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Comment: C: TCGA exon quantification file
... Hi, I know this is an old post but I came about it as I have a similar problem. I'm dealing with level 3 exon quantification data and I'm trying to map the co-ordinates to transcript ID. The problem I'm having is that some of the co-ordinates aren't annotated or even in the gtf file. I know the TCG ...
written 21 months ago by Newbie0
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Comment: C: TCGA raw counts DexSeq
... Great, thank you, much appreciated :-) Also one more question, my gtf file needs to be converted to gtf for DexSeq which is fine because they provide a python script to do that, so would I better to extract the exon co-ordinates and transcript ID's from the gff file, and what would be the best way t ...
written 21 months ago by Newbie0
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Comment: C: TCGA raw counts DexSeq
... Should I convert my RNA seq file to a bed file first? And regards using bedtools how would I use that to map both files? Do you have any examples on how to do it? Apologies for the questions, I'm new to bioinformatics but have experience using basic bash commands and R and this is probably an obvio ...
written 21 months ago by Newbie0
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Comment: C: TCGA raw counts DexSeq
... this is the file I'm currently working with, thought it might help understand what I mean. It's level 3 Data exon quantification data from the TCGA Hybridization REF TCGA-3C-AAAU-01A-11R-A41B-07 TCGA-3C-AALI-01A-11R-A41B-07 TCGA-3C-AALJ-01A-31R-A41B-07 exon raw_counts raw_counts raw_counts raw_cou ...
written 21 months ago by Newbie0
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Comment: C: TCGA raw counts DexSeq
... hi, thanks for replying. I'll have a look at doing that, thank you. Although I'm not sure if it will work, the main issue I'm having is getting a transcript ID, because each row in my data file corresponds to one exon giving the chromosome start and end so I'm having trouble understanding how I can ...
written 21 months ago by Newbie0
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TCGA raw counts DexSeq
... Hi, I have a question regarding input file into DexSeq. I've read the DexSeq manual and see that it requires a SAM/BAM file to generate the counts file. The problem is that I have neither the SAM/BAM file as I have taken RNASeq level 3 data from the TCGA site which contains the chromosome start an ...
dexseq tcga rna-seq written 21 months ago by Newbie0 • updated 21 months ago by H.Hasani640

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