User: rbj

gravatar for rbj
rbj30
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30
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New User
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Last seen:
5 months, 2 weeks ago
Joined:
6 months, 2 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 5 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 5 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 5 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 5 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 5 months ago by rbj30 • updated 5 months ago by Jennifer Hillman Jackson23k
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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 6 months ago by rbj30 • updated 6 months ago by Mo Heydarian790

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