User: amaheras7091

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amaheras709110
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Posts by amaheras7091

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Getting Figures from R with Galaxy DESEQ2 output?
... I discussed the issue with my research advisor, and we both agree that such a feature would be incredibly beneficial for our intentions to publish with our data we have thus far analyzed through use galaxy.com. I shall create a github accordingly. Thank you for your assistance. ...
written 20 months ago by amaheras709110
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Getting Figures from R with Galaxy DESEQ2 output?
... Hi, So this summer I ran a bioinformatics workflow on differential gene expression in three samples in galaxy (shown below) and now I want to use R to get publishable figures. If I have the DESeq2 results output, is there a way to view and manipulate these tabular files on R and create graphs/figur ...
publication statistics graphs figures rna-seq written 20 months ago by amaheras709110 • updated 20 months ago by Jennifer Hillman Jackson25k
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Comment: C: DanRer10 Effective Genome Size?
... Hi, On the UCSC Genome Browser (http://genome.ucsc.edu/cgi-bin/hgTables), there are several tracks that are under "Variation and Repeats" (Interrupted Rpts, Microsatellite, RepeatMasker, Simple Repeats, WM + SDust) and I looked at the summary statistics for each. In order to choose which one(s) to ...
written 23 months ago by amaheras709110
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Comment: C: Cuffmerge fails to merge gtf files
... I wonder if it makes a difference if you try merging both the assembled and the skipped transcripts ...
written 23 months ago by amaheras709110
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Answer: A: Cuffmerge fails to merge gtf files
... Hi, Are you trying to merge just the assembled transcripts, or the assembled transcripts and the skipped transcripts? ...
written 23 months ago by amaheras709110
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DanRer10 Effective Genome Size?
... Hi, I'm trying to use bamCoverage to convert my TopHat bam files into bigwig files for visualization on UCSC genome browser. bamCoverage asks for the Effective Genome Size and if I'm using the zebra fish DanRer10 genome, does anyone know what the effective genome size would be for that? Also, this ...
galaxy tophat rna-seq written 24 months ago by amaheras709110 • updated 24 months ago by Jennifer Hillman Jackson25k
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Cuffdiff input into Cummerbund error?
... Hi all, So I completed a standard workflow using top hat through cuffdiff in order to find differentially expressed genes. On cuffdiff, I clicked the option to have the sqlite file output compatible with Cummerbund; however, when I input all of the sqlite files into Cummerbund I received a fatal er ...
galaxy cufflinks rna-seq written 24 months ago by amaheras709110
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How to extract genes.gtf file from uncompressed gz file
... Hi, I am trying to use the DanRer10 UCSC zebrafish genome file found on the illumina website under iGenomes in my RNA-seq Cufflinks workflow. The file downloaded as a compressed tar.gz file, so I uncompressed it with 7-zip (a program downloaded from the internet) which gave me an uncompressed gz fi ...
galaxy cufflinks rna-seq written 2.0 years ago by amaheras709110 • updated 2.0 years ago by Jennifer Hillman Jackson25k

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