User: nashedm

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nashedm10
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United States
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2 years, 11 months ago
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Posts by nashedm

<prev • 11 results • page 1 of 2 • next >
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Mutliple UCSC gene names in RStudio Data Table
... Hi there, I am using the cummeRbund package in R Studio on my personal computer to analyze differentially expressed genes using cuffdiff output files from Galaxy. When extracting the list of genes that are differentially expressed, I initially get only the XLOC names. To get the UCSC names, I do t ...
r studio xloc gene name ucsc cummerbund written 2.9 years ago by nashedm10 • updated 2.9 years ago by Jennifer Hillman Jackson25k
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Visualizing CuffDiff Data
... Hi,  I've run an RNAseq experiment to look for differentially expressed genes using CuffDiff. I've been using the Tuxedo protocol thus far and wanted to continue by using CummeRbund to visualize my results and create graphics for publication, but I noticed that CummeRbund is not included in Galaxy. ...
cuffdiff rna-seq galaxy cummerbund written 2.9 years ago by nashedm10 • updated 2.9 years ago by Jennifer Hillman Jackson25k
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Comment: C: Cuffdiff not working in Galaxy
... Sorry I'm not sure how to use Gist. When I expand the files, there's a blue information notice that says "The job creating this dataset has been resubmitted". Underneath that it says "tool error. An error occurred with this dataset:" but there's no more information given. When I click on the icon fo ...
written 3.0 years ago by nashedm10
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Cuffdiff not working in Galaxy
... Hi, I'm trying to run cuffdiff as part of an RNA-seq project, and it's not working. I've tried leaving it to run overnight 3 times now and every time it starts the job but ends up giving me a tool error for all the files it's trying to create.  I'm using a cuffmerge assembly in my transcript input ...
cuffdiff galaxy cufflinks software error rna-seq written 3.0 years ago by nashedm10
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Comment: C: Locally cached sequence not detected from DBkey in cuffmerge when using mm10
... I'm still having the same problem as well. 2 days ago I think it worked briefly- I was able to choose "locally cached" but there was no drop-down menu to select a genome. I assumed maybe it just automatically detects the appropriate genome based on the cufflinks files or something- I'm not sure. But ...
written 3.0 years ago by nashedm10
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Comment: C: Locally cached sequence not detected from DBkey in cuffmerge when using mm10
... Hi Jen, I'm having the same problem as Max. I'm not sure if it has been resolved yet but it's not working for me. I'm trying to use the built in mm10 reference genome as my sequence data in Cuffmerge (also to then do differential analysis with Cuffdiff), but nothing is showing up in "locally cached ...
written 3.1 years ago by nashedm10
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Comment: C: Combining Reads from 2 Lanes
... Thanks for the reply, Philip.  I'm not sure that's right though. The concatenate datasets tool merges "tail to head". I actually used this tool as well because I for each lane I had multiple FASTQ files that were basically continuations of each other- as the machine sequenced it created separate fi ...
written 3.1 years ago by nashedm10
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Combining Reads from 2 Lanes
... Hi, I'm running an RNA-seq analysis to look for differentially expressed genes. I'm using sing-end reads at 50bp from an an Illumina HiSeq Rapid V2 machine.  I have 3 conditions with 6 biological replicates in each. Also, for each biological replicate, I have 2 FASTQ files, one from each lane. I g ...
bam samtools galaxy tophat rna-seq written 3.1 years ago by nashedm10 • updated 3.1 years ago by Philipe Moncuquet40
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Comment: C: Multiple FASTQ files per replicate
... Thanks Jen, These are single-end sequences. I clarified with the technician and she would not treat sequences from 2 lanes for one sample as technical replicates (because data was not collected twice from the same prep). Rather, she said to treat the data from the 2 lanes as subsets of the same sequ ...
written 3.1 years ago by nashedm10
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Comment: C: Multiple FASTQ files per replicate
... Thanks Jen, These are single-end sequences. I clarified with the technician and she would not treat sequences from 2 lanes for one sample as technical replicates (because data was not collected twice from the same prep). Rather, she said to treat the data from the 2 lanes as subsets of the same se ...
written 3.1 years ago by nashedm10

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