User: pjferrandi

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Posts by pjferrandi

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Comment: A: Odd Fastq sequences; 50% Aligned more than once
... Indeed, these data were small RNA seq specific data. My PI is in the process of getting the correct sequence files, which will hopefully pan out nicely for us. Thanks to everyone for your help! ...
written 7 weeks ago by pjferrandi0
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Comment: C: Odd Fastq sequences; 50% Aligned more than once
... My mistake! I am attempting to map to a reference via HISAT2 and/or STAR...for now I've just attempted HISAT2 to the reference mouse genome. Following this, I used htseq-count to get the read counts for each identified gene/transcript. This worked perfectly fine on the dataset I pulled from SRA (not ...
written 7 weeks ago by pjferrandi0
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Comment: C: Odd Fastq sequences; 50% Aligned more than once
... Lol, I really wish I understood what you mean. Should I contact the sequencing company for clarification on what these files actually are? The other set of files I'm comparing these to, I downloaded from SRA and they work perfectly when I run them through my Galaxy workflow...I'm not exactly sure wh ...
written 7 weeks ago by pjferrandi0
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Odd Fastq sequences; 50% Aligned more than once
... Hello all. I'm REALLY trying to get DEG analysis done for my PI with essentially no experience and no guidance. I'm using Galaxy and attempting to assemble the fastq files received via sequencing and am getting very strange results. FastQC shows very odd GC%: The raw read file itself looks odd to ...
assembly sequence rna-seq alignment written 7 weeks ago by pjferrandi0

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