User: andrewzlobin

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andrewzlobin10
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Posts by andrewzlobin

<prev • 20 results • page 1 of 2 • next >
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Cuffdiff -splicing analyses produced no value
... Caffdiff works fine in all area, except splicing: table produced contain no value, just "0". What can be a problem? ...
rna-seq written 6 days ago by andrewzlobin10
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Cuffdiff crashed if I try to use option "Generate SQLite"
... I am running Cuffdiff on my data, It runs fine, but if I am adding option "Generate SQLite" it crashed. What's the problem? ...
rna-seq written 6 days ago by andrewzlobin10
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RNA STAR: Fatal INPUT FILE error, no valid exon lines in the GTF file: /galaxy-repl/main/files/026/062
... Hellow Running Star, no go, Jul 06 01:00:55 ..... started STAR run Jul 06 01:00:55 ..... loading genome Jul 06 01:02:17 ..... processing annotations GTF Fatal error: Matched on FATAL ERROR Fatal INPUT FILE error, no valid exon lines in the GTF file: /galaxy-repl/main/files/026/062 What;s can be wr ...
galaxy software error rna-seq written 10 days ago by andrewzlobin10
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Answer: A: Star-Fusion: A last-matching gene pairs file - in Galaxy you can create such fil
... I am lost I can not find out how I created genes.gft, neither AABR07.fasta for rat. Could you explain please? Thanks Andre ...
written 11 days ago by andrewzlobin10
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Answer: A: Star-Fusion: A last-matching gene pairs file - in Galaxy you can create such fil
... Dear Jennifer, My question is: When I ran RNA STAR I could not "Use genome reference with builtin gene model", as "Select reference genome" is empty and, so I use Genome reference WITHOUT builtin gene model: Select reference genome Rat Jun.2014 (RGSC 6.0/rn6) (rn6). Gene model (gff3,gtf) file for ...
written 12 days ago by andrewzlobin10
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Answer: A: Star-Fusion: A last-matching gene pairs file - in Galaxy you can create such fil
... Thanks a lot. It did not work so far. I am afraid this is RNA STAR program problem. When I ran RNA STAR I took Use a build in index I could not "Use genome reference with builtin gene model", as "Select reference genome" is empty, So I use Genome reference WITHOUT builtin gene model: **Select refe ...
written 14 days ago by andrewzlobin10
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Answer: A: Star-Fusion: A last-matching gene pairs file - in Galaxy you can create such fil
... Thanks a lot, But it looks to me that locally cashed sequences for Rat includes only rn5. Is this correct? Thanks Andre ...
written 16 days ago by andrewzlobin10
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Star-Fusion: A last-matching gene pairs file - in Galaxy you can create such files with the ncbi_blast_plus tool suite containing blastn: ....
... I am running Star-fusion on rat genome Position: A last-matching gene pairs file - in Galaxy you can create such files with the ncbi_blast_plus tool suite containing blastn: https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus not clear to me. I tried to generate the file like advis ...
fusion galaxy blast ncbi star written 16 days ago by andrewzlobin10
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Answer: A: htseq-count crashed again and again
... Sorry I found the problem. Thanks Andrew ...
written 24 days ago by andrewzlobin10
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Answer: A: htseq-count crashed again and again
... With the most resent rat annotation file I was able to run HTseq-count on my data. But after that when I try to run output files on DESeq2 it crashes:" Fatal error: An undefined error occurred, please check your input carefully and contact your administrator. Error in `row.names<-.data.frame`(`*t ...
written 24 days ago by andrewzlobin10

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