User: rbj

gravatar for rbj
rbj30
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30
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New User
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Last seen:
10 months, 3 weeks ago
Joined:
11 months, 3 weeks ago
Email:
r**@liv.ac.uk

Posts by rbj

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Cufflinks Gene Transcripts
... Thank you Jen, OK had missed the MT chromosomes. I didn't find an easy safe way to change this (even following the link!), so wrote a Matlab script to change all the starting chromosome, hopefully appropriately. Seems to work now. Everything seems to have worked, but will cross check with the dat ...
written 10 months ago by rbj30
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Comment: C: Cufflinks Gene Transcripts
... So to conclude with this particular issue I've had. The error was indeed in the rat.GFF3. Because the file comes as chromosomes labelled simply by a number or letter (not chrx) as required, I wrote a script to pre-pend the "chr"s. For some reason this did the first few and not the whole lot, so Cu ...
written 10 months ago by rbj30
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Comment: C: Cufflinks Gene Transcripts
... ...and, if anyone is following this saga in real time :-) I have now established that when I converted my "1"s to "chr1" etc.... (in Matlab) I only seem to have done the chromosome 1's not all the others. Correcting this now. I expect that was my fault. I will update when I have fixed my appending ...
written 10 months ago by rbj30
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Comment: C: Cufflinks Gene Transcripts
... Thank you very much Jen, I am still diagnosing; firstly (for everyone's info), this is rat tissue so the genome is (release 6) is installed in usegalaxy.org, but the annotation reference is one I prepared. So that is likely to be the error. I believe it is sorted, and I am pretty sure the bam is. ...
written 10 months ago by rbj30
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Cufflinks Gene Transcripts
... Hi I have been experimenting with Bowtie and Cufflinks and I now reach a point where it appears to work; but I think there is a subtle error. I don't find ENOUGH gene hits. So (1) I got the same dataset professionally analysed by GATC and they returned 20k genes, but when I do it I get 2k. (2) Whe ...
bowtie cufflinks genes rna-seq written 10 months ago by rbj30 • updated 10 months ago by Jennifer Hillman Jackson25k
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Server Statuses or Queue times
... I just wondered whether there were any real time server status pages or estimated queue times? If not it might be a useful feature. On sunday, as one would guess, it took me only a few minutes to discover my analysis had failed (it will be my error for sure)). Now it is about 24hrs so far. regards ...
queue written 11 months ago by rbj30 • updated 11 months ago by Mo Heydarian790

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