User: m.maleszewska

gravatar for m.maleszewska
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Location:
Netherlands
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3 years, 3 months ago
Joined:
3 years, 8 months ago
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Posts by m.maleszewska

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Gene_short_name missing in CuffDiff output files
... Thank you Jen! This is very helpful! The file I found is however only ~100Mb, I hope that's correct. I will then try to use it with CuffMerge and then do CuffDiffs again. Within CuffDiff, there is also an option to use Reference sequence, which I normally set at Locally cached (and then it automat ...
written 3.5 years ago by m.maleszewska20
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Comment: C: How to upload a genome from igenomes to Galaxy?
... Thank you for the information! Could you advise what source of genome is the best then to use with the Tuxedo pipeline at Galaxy? I at first uploaded a gtf file from UCSC with ensembl genes instead of one of igenomes, but in the end I missed the gene names in my CuffDiff output files, which was ver ...
written 3.5 years ago by m.maleszewska20
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Comment: A: How to upload a genome from igenomes to Galaxy?
... Thank you! The uploading worked, but I'm not sure if the unpacking did, as I have trouble using the file and the contents don't look right... It Autodetects it as a gtf, but I can't use it... I think based on: ftp://ussd-ftp.illumina.com/README.txt , that it actually contains different sorts of fil ...
written 3.5 years ago by m.maleszewska20
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Comment: C: How to upload a genome from igenomes to Galaxy?
... I think I managed to upload a zipped file (tar), but how do I unpack it to be able to use it? ...
written 3.5 years ago by m.maleszewska20
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How to upload a genome from igenomes to Galaxy?
... As above - how can I directly upload a reference genome from http://cufflinks.cbcb.umd.edu/igenomes.html to a history at Galaxy? Thank you in advance, Best, Monika ...
gtf reference tuxedo rna-seq written 3.5 years ago by m.maleszewska20
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Answer: A: Gene_short_name missing in CuffDiff output files
... Similar discussion and perhaps a solution (I started it again here, because the fora did not seem connected, unless I'm wrong?): https://www.biostars.org/p/107585/#108172 . ...
written 3.5 years ago by m.maleszewska20
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Answer: A: Gene_short_name missing in CuffDiff output files
... Hi Ahdee, Thank you for your tip! I am worried though that if this is messed up, perhaps something else is wrong with my files too that I don't see... Also, cummeRbund uses this column, e.g. if I make a heatmap, it puts all the ENSTs at the side of it and it looks terrible (which I can fix by ommi ...
written 3.5 years ago by m.maleszewska20
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Gene_short_name missing in CuffDiff output files
... Dear All, I ran Tuxedo at Galaxy (public, online), using TopHat2-Cufflinks-Cuffmerge-Cuffdiff. I expected my Cuffdiff output to contain gene_name, so that I could directly identify genes in downstream analyses. However, it seems to be missing and I only have a list of transcript ids (all isoforms) ...
cuffdiff cufflinks gene_name rna-seq written 3.5 years ago by m.maleszewska20 • updated 3.5 years ago by Jennifer Hillman Jackson23k
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Comment: C: FastQC doesn't work after Splitter
... Thank you Jen, as always very clear and helpful! All best, Monika ...
written 3.6 years ago by m.maleszewska20
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TopHat for Illumina or TopHat2 for Illumina data - what's the difference?
... Hello, I wonder if I should use TopHat for Illumina or TopHat2 to align data that come from Illumina? Is there a difference? Or is TopHat2 simply a newer version and I should use that? All best, Monika ...
alignment tophat rna-seq written 3.6 years ago by m.maleszewska20 • updated 3.6 years ago by Jennifer Hillman Jackson23k

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