User: a.morris

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a.morris40
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a*******@imperial.ac.uk

Posts by a.morris

<prev • 9 results • page 1 of 1 • next >
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Comment: A: Get Data > EBI SRA (ENA) incorrectly assigning fastqsanger instead of fastqsange
... Thankyou for the quick workaround. yes these metafiles should have been formatted as compressed files with a .gz suffix ...
written 9 weeks ago by a.morris40
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Get Data > EBI SRA (ENA) incorrectly assigning fastqsanger instead of fastqsanger.gz datatype, OPEN, read for workaround
... Dear Advisor You were very helpful with overcoming my Galaxy problems at the end of last year and Im hoping you are still in a position to help again. I am testing two downloaded files (paired end) for SRX1725724 via ENA. (Error 1) When I try FastQC, the following error msg is returned: “ ...
ena galaxy datatype fastqsanger.gz ebi sra written 10 weeks ago by a.morris40 • updated 3 days ago by Jennifer Hillman Jackson25k
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Use of slice to estimate rpkm/fpkm
... When estimating transcript levels from RNA Seq data that have been normalized using rpkm or fpkm, would the slice SAMtool (which manually sets a list of coordinates and extracts the data say for the few genes selected out of the whole transcriptome) differ from the results obtained from the (unslice ...
slice samtools rna-seq fpkm/rpkm written 8 months ago by a.morris40 • updated 8 months ago by Jennifer Hillman Jackson25k
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Comment: C: C: Bias Correction : Locally cached human reference sequence data
... Just found out that the Cufflinks detects only hg_g1k_v37 and not hg19, which solves the problem ...
written 10 months ago by a.morris40
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Using DEXSeq count on a sliced bam or sam file
... Using DEXSeq count on a sliced bam or sam file does not seem to run properly. The output file reads eg., as follows: ambiguous 0 _ambiguous_readpair_position 0 _empty 9893 _lowaqual 0 _notaligned 0 The sliced file had the hg19 genome database . ...
rna-seq written 10 months ago by a.morris40 • updated 10 months ago by Jennifer Hillman Jackson25k
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C: Bias Correction : Locally cached human reference sequence data
... Hello Jennifer, your most answer correctly identified a problem with Cuffdiff returning red boxes last week. However this week I am using Cufflinks. Under the Biass correction option (Yes) and cached Ref sequence data, the using reference genome only returns "no options available. Last time I ...
cufflinks written 10 months ago by a.morris40 • updated 10 months ago by Jennifer Hillman Jackson25k
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Bias Correction : Locally cached human reference sequence data
... For a cufflinks run, Galaxy detected up human (homo Sapiens) hg19 for the locally cached reference sequence data but , follwoing execution, it returned a pink error msg: "Parameter index requires a value, but has no legal values defined." ...
cufflinks written 10 months ago by a.morris40 • updated 10 months ago by Jennifer Hillman Jackson25k
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Jobs running for over 24 hours ( still unfinished) that previously took a few hours?
... I have started to run Tophat twice for 4 datasets. Both attempts have resulted in the jobs still running 24 hours later. In the past such jobs took a few hours not over 24 hours. No error messages are shown ...
galaxy rna-seq written 10 months ago by a.morris40 • updated 10 months ago by Jennifer Hillman Jackson25k
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Research on RNA SEQ
... Please recommend instructions for day to day handling of the disk space in galaxy. Ive only done 3 out of 38 samples and its full, so the samples in history need to managed on a weekly basis. ...
quota space galaxy written 12 months ago by a.morris40 • updated 12 months ago by Martin Čech ♦♦ 4.8k

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