User: ea11g0

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ea11g00
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Posts by ea11g0

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Comment: C: Issue with easyRNASeq
... Hi Nico, That is great thanks! I have finally managed to get it to work and to get a count table at the end of it. Thanks a lot for all your help and if I run into any other problems with easyRNASeq, I will let you know.   Thanks, Elie   ...
written 4.3 years ago by ea11g00
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Comment: C: Issue with easyRNASeq
... Hi Nico, Thanks for that. I have tried downloading curl and using curl("https://microasp.upsc.se/root/upscb-public/raw/master/src/R/createSyntheticTranscripts.R"). The output from that is:                                                                                description "https://microas ...
written 4.3 years ago by ea11g00
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Comment: C: Issue with easyRNASeq
... Hi Nico, I have had a quick look at your response, but I can't seem to create a synthetic transcript file. I am following the details on the link you provided, however, this is what I am getting:   > source("https://microasp.upsc.se/root/upscb-public/raw/master/src/R/createSyntheticTranscripts ...
written 4.3 years ago by ea11g00
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Comment: C: Issue with easyRNASeq
... Hi Nico,   That's great thanks for figuring out what was wrong for me. I shall have a proper read through the links and the working solution when I get into the office tomorrow, but it is great to finally know what was wrongs.   Thanks, Elie ...
written 4.3 years ago by ea11g00
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Comment: C: Issue with easyRNASeq
... Hi Nico, Thanks for that, I have sent you an email. Thanks, Elie ...
written 4.4 years ago by ea11g00
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Comment: C: Issue with easyRNASeq
... Hi Nico, Yea it should be no problem to send you an excerpt of the BAM files. Do you want the header and 1M lines for both files? For the header do you want the output from: samtools view -H 01_v2.bam How do I get the first 1M lines for you?   Thanks, Elie   ...
written 4.4 years ago by ea11g00
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Comment: C: Issue with easyRNASeq
... Hi, I will keep a look out for the new version of easyRNASeq once it becomes accessible through biocLite(). The gtf file was from ENSEMBL. I retried the whole thing with a different gtf file that I got from gencode, and this is the error that I get: Warning messages: 1: In FUN(X[[i]], ...) : Bam ...
written 4.4 years ago by ea11g00
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Comment: C: Issue with easyRNASeq
... Hi, Thanks for that. I have spoken to the administrator and he has managed to install R 3.2.1 onto the system, and this is now my sessionInfo():   > sessionInfo() R version 3.2.1 (2015-06-18) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server release 6.3 ...
written 4.4 years ago by ea11g00
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Comment: C: Issue with easyRNASeq
... Hi, Thanks for the reply. Does version 2.4.4 of easyRNASeq install on R 3.1.2? I don't think I can update the version of R that I have as I am not in control of the UNIX environment that I am using to run R and analyse my RNAseq data. Thanks ...
written 4.4 years ago by ea11g00
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Issue with easyRNASeq
... Hi, So I'm running easyRNASSeq on a couple of bam files that I have, before I do it on all 40 samples in order to get a count table for the samples. However, I keep getting an error and am unsure as to why. If I could get any help that would be great. Below is the script that I am using: > lib ...
easyrnaseq error written 4.4 years ago by ea11g00

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Popular Question 4.0 years ago, created a question with more than 1,000 views. For Issue with easyRNASeq

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