User: vasioukhin

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vasioukhin0
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Posts by vasioukhin

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Comment: C: Finding exogenous transcripts in RNA-Seq bam files
... Dear Jennifer, Thank you for taking your time to answer my questions.I think I am missing something important.Are you explaining how to make a GTF file from a given sequence?GFP and Cre sequences are not in any genomes. What do I blast them against? Wow, it seems that this is such an easy and useful ...
written 20 months ago by vasioukhin0
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Comment: A: Finding exogenous transcripts in RNA-Seq bam files
... Yes, the reads are from RNA. ...
written 20 months ago by vasioukhin0
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Answer: A: Finding exogenous transcripts in RNA-Seq bam files
... Thanks Jen. I think what we want to do is something that will be useful for almost all researchers working with RNA-Seq. Our reads are from mouse cells and mouse tissues. We mapped them against mm10 genome and generated GTF and BAM files. What would be the way to generate GTF file for Cre and GFP us ...
written 20 months ago by vasioukhin0
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Finding exogenous transcripts in RNA-Seq bam files
... Hello, What is the easiest way to find and count reads for exogenous transcripts (Cre, GFP, etc.) in RNA-Seq bam files using Galaxy? These transcripts are not in normal genomic databases, but I can make Fasta files for them. Thank you, Valeri ...
gfp transcripts count reads cre rna-seq written 20 months ago by vasioukhin0

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