User: oma219

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oma21930
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Posts by oma219

<prev • 43 results • page 1 of 5 • next >
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Blast2Go - Running Jobs in the Background
... Hello, I'm new to the Blast2Go platform and I had a basic question. If you are using the java application, is there a way to run the blast and interproscan without keeping the application window open the entire time? Like a background job? Thanks, Omar ...
blast written 19 months ago by oma21930
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Issues with building an index in salmon
... Hello, I was building an index with Salmon and had some of these warnings come up with the index was being built. Are these warnings usually indications that the wrong file was used to make the index? Thanks. /home/ubuntu/software/Salmon-0.8.2_linux_x86_64/bin/salmon index -t /home/ubuntu/da ...
software error written 23 months ago by oma21930
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Best Programs for transcript counts
... Hello, I just finished producing gene counts and I was going to move into transcript counts. I think featureCounts and cufflinks are able to do transcript counts but I just wanted to get other opinions on programs they found to useful when it came to producing transcript counts? Thanks. ...
sequence rna-seq written 23 months ago by oma21930 • updated 23 months ago by Carlos Caicedo130
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Comment: C: Error when installing cufflinks
... I tried setting $BAM_ROOT by just writing $BAM_ROOT=/home/ubuntu/software/samtools-1.4.1/ but it keeps saying its not a valid directory. ...
written 24 months ago by oma21930
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Error when installing cufflinks
... Hello, I had this error when trying to install cufflinks and it seems like a common error when I search around but I'm still not sure how to fix it. None of the methods I have found have worked for me. I installed samtools in folder and provided the path to that folder with the --with-bam option bu ...
software error written 24 months ago by oma21930 • updated 23 months ago by Jeffin Rockey1.1k
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Comment: C: Trying to use the gff_to_gtf utiilty in genomeTools
... I keep getting this error. Do you know what this means? ubuntu@ip-172-31-19-217:~/software/genometools-1.5.9$ make prefix=/usr 64bit=no cairo=no install grep: src/tools/*.c: No such file or directory grep: src/tools/*.c: No such file or directory grep: src/tools/*.c: No such file o ...
written 24 months ago by oma21930
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Trying to use the gff_to_gtf utiilty in genomeTools
... Hello, I downloaded the genomeTools package so I could use the utility gff3_to_gtf utility but I'm having trouble finding it. I have looked at the documentation online and the READMEs but I cannot seem to locate the script. Does anyone know where it would be located? Thanks. ubuntu@ip-172- ...
genome written 24 months ago by oma21930
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Comment: C: Contents of .gff3 files necessary for gene counts
... ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | ...
written 24 months ago by oma21930
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Differences between ensembl gtf files and gff3 file
... Is the gene_id attribute in the GTF files analogous to the Name attribute in the .gff3 file? Because both featureCounts and htseq-count have the default id attribute as gene_id but I have .gff3 so I'm trying to figure out what I should change it to? Thanks. ...
sequencing written 24 months ago by oma21930 • updated 24 months ago by dariober10k
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Contents of .gff3 files necessary for gene counts
... Hello, I having second thoughts about how I made my annotation file I just wanted to get second thoughts. So originally, I had an annotation file in the .gff3 format that whenever I ran it with htseq-count or featureCounts would give me an error since not every line had a gene_id tag? So for gettin ...
rna-seq sequencing written 24 months ago by oma21930 • updated 24 months ago by WouterDeCoster38k

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