User: mvinas

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mvinas20
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Posts by mvinas

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Answer: A: Less reads when uploading to galaxy
... Thanks Jen, I found the problem. Galaxy was recognizing the wrong format. I set the correct type of format (fastq.bz2) before loading the data and it worked!. Maria Vinas ...
written 3 months ago by mvinas20
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Less reads when uploading to galaxy
... Hello, I am trying to upload files which contains, each, about 40 millions of reads (~2GB each, file format: fastq.bz2). But when I upload them from the ftp server, not all reads, and only some of them (only 4200 sequences) appears in the file in Galaxy. What can be the reason? Thank you in advan ...
rna-seq written 3 months ago by mvinas20
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Heatmap using cummeRbund
... Hello, I want to do a heatmap using cummeRbund. Is it possible to select a set of genes (for example only the significantly expressed ones) or it is only possible to do it one by one? Thanks in advance, Maria Vinas ...
rna-seq written 3 months ago by mvinas20
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Comment: C: fastq.gz data - help for changes that impact upload (any source), history conten
... Many thanks Jen, I am "Grooming" each data first and then prepare the "dataset collection" and it worked. I did not have to uncompressed the .fastq.gz files and now TopHat analysis and next steps are faster than before. Maria ...
written 8 months ago by mvinas20
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Answer: A: fastq.gz data - help for changes that impact upload (any source), history conten
... Thank you Jen, In my case, FASTQ Groomer did not recognize *fastq.gz* data when is a "dataset collection", it recognizes only "single" *fastq.gz* data. So, I had to uncompress the data but, because is very large, TopHat is taking more than 2-3 days, Is this normal? Before was around 2-3 hours. Th ...
written 8 months ago by mvinas20
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fastq.gz data - help for changes that impact upload (any source), history contents, and tool usage
... Hello, I am downloading the data from SRA to Galaxy directly, but it seems Galaxy can not unzipped the files automatically. I did it many times before and it was working, but not now. There is another way how to unzipped the files? Thanks, Maria ...
fastq.gz fastqsanger datatype fastqsanger.gz fastq written 8 months ago by mvinas20
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htseq-count unknown error
... I am trying to use htseq-count tool for gene quantification, but I have this error: **"Fatal error: Unknown error occured: Error occured when processing GFF file (line 11 of file /galaxy repl/main/files/018/552/dataset_18552527.dat): Feature id1 does not contain a 'gene_id' attribute [Exception typ ...
rna-seq written 8 months ago by mvinas20
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TopHat input data
... Hello, I am trying to analyze ARN-seq, but when I use TopHat my data is not recognized and I can not include them in the analysis. Is it because they do not have "Sanger-scaled quality values with ASCII offset 33"?? or there is another option?. It says: "no fastqsanger dataset available". But data ...
fastqsanger input qa tools fastq written 9 months ago by mvinas20 • updated 9 months ago by Jennifer Hillman Jackson23k

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