User: jer364

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jer3640
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Posts by jer364

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Comment: C: bowtie2: Print only Alignment Summary?
... Thank you! This worked! ...
written 7 days ago by jer3640
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bowtie2: Print only Alignment Summary?
... I'm assembling transcriptomes and am trying to map my reads back to my contigs using bowtie2. Is there a way to only print the summary statistics or ignore alignment information? Otherwise summary file is hundreds of gigs. Thanks for any help! ...
alignment rna-seq written 15 days ago by jer3640
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Answer: A: Manually Search Sam/Bam File
... Found an easy solution. Just read it into R using Rsamtools! ...
written 12 weeks ago by jer3640
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Comment: A: Manually Search Sam/Bam File
... Hi Richard, I guess I should say I originally used kraken2 since I was already classifying the bacterial sequences (it is SRA Metagenomic data), and then made a separate viral database. however, I didn't get any assigned hits, so I tried blasting, the results of which I got impatient for (been abou ...
written 12 weeks ago by jer3640
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Manually Search Sam/Bam File
... Hi All, I would like to map short reads against a reference database for viral discovery using bowtie2. However, since I don't know what I'm looking for, I need a way to parse the output to filter out spurious hits and focus on more interesting things. I was hoping there was a way to format a sam/b ...
alignment written 12 weeks ago by jer3640
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Comment: C: Unrecognized Sequence in NGS reads
... Sorry, I forgot the index file wasn't included in the SRA upload. The files for that sample can be found on their GitHub https://github.com/AbateLab/SiC-seq linked in an issue posted by jessieren. ...
written 3 months ago by jer3640
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Comment: C: Unrecognized Sequence in NGS reads
... Right now I'm working with a single sample, SRR5202186, to get a pipeline established. ...
written 3 months ago by jer3640
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Comment: C: Unrecognized Sequence in NGS reads
... Hi @genomax, These are unpaired reads. The only files are the R1 and Index files. So Read 1 contains what should be the genomic info, and Read 2 has the 15 bp barcode sequence. ...
written 3 months ago by jer3640
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Unrecognized Sequence in NGS reads
... Hi All, I downloaded some SRA files from a paper that used single cell sequencing with unique barcodes for each cell. I took a closer look at some of the sequences that didn't map to a reference genome (the sample was a community standard so species were known) and hoped someone could help me inter ...
sequencing written 3 months ago by jer3640

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