User: azadjali

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azadjali0
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Posts by azadjali

<prev • 7 results • page 1 of 1 • next >
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Comment: C: tophat is not responding
... Thank you dear Jennifer, I got your point. Just to tell you that the tophat issue appeared again (its really annoying) as I ran new dataset that stuck with tophat since morning-hope it wont take days like last time and I hope the team can solve the issue as soon as possible. Thank you again. Thank ...
written 23 months ago by azadjali0
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Comment: A: tophat is not responding
... Sorry guys it start working again but as usual slow and late respond. what I did after 3 days of waiting, I deleted my complete history and re run my datasets and it works ...
written 23 months ago by azadjali0
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tophat is not responding
... Hi I have large dataset and I want to get the differential expression but the tophat is not responding, its not running, it has been now 3 days. In one of the dataset the colour changed from grey to yellow (the dataset is running) but green color never appeared - I delete it and re run the same fi ...
usegalaxy.org job tophat queue written 23 months ago by azadjali0 • updated 23 months ago by Jennifer Hillman Jackson25k
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Answer: A: quantity of each replicate / id conversion
... Thank you dear Jennifer I think as you said the output of Cufflinks [appears in history as a file of: gene expression under the column of FPKM] but is there any way to read the raw counts of those genes instead of FPKM. and thank you for the site iGenomes: http://support.illumina.com/sequencing/ ...
written 2.4 years ago by azadjali0
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quantity of each replicate / id conversion
... Hi I need an information about the quantity of genes in each replicates how to do it I am using two different types of mice WT and knock out, the samples for both types were taken at 5 different age groups and there are 3 replicates for each. my targets will be to get the differential expression wh ...
galaxy written 2.4 years ago by azadjali0
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Answer: A: removing of duplication in RNA seq
... Thank you for your Kind reply dear Jennifer I think I will follow the same steps in the recommended method [Cufflink version < 2.2.0 still supported]  I wish Galaxy have tools for Cummerbund  and shows some videos how to run it  thank you again ...
written 2.8 years ago by azadjali0
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removing of duplication in RNA seq
... Hi I am new in bioinformatics and in Galaxy too so please bear with me Soon I will have RNA seq samples (single reads) for wild type and mutant, and my target is to get expression levels between them. This is my pipeline :- Groomer → Filtration (clipping, filtration quality)→ Alignment (Tophat) ...
galaxy written 2.8 years ago by azadjali0

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