User: achamess

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achamess50
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Posts by achamess

<prev • 27 results • page 1 of 3 • next >
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Comment: C: Single-nucleus RNA-seq processing (10x) with Pseudoaligners (Kallisto)
... Thanks! Can the same cDNA/intron index be used with Kallisto for processing of bulk nuclear RNA-seq too? ...
written 10 days ago by achamess50
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Single-nucleus RNA-seq processing (10x) with Pseudoaligners (Kallisto)
... I currently use CellRanger on single nucleus RNA-seq data using the pre-mRNA reference that they advise. https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references I want to try using Kallisto Bustools for increased processing speed. However, I haven't ...
scrna-seq kallisto rna-seq written 10 days ago by achamess50 • updated 10 days ago by Lior Pachter370
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Answer: A: How To Plot Rarefaction/Saturation Curve Based On Bam File Generated By Tophat?
... Are there any readily available tools or scripts to perform this analysis? RSeqQC doesn't do it for me. I'd like to produce a graph like this: https://cofactorgenomics.com/1-graph-will-give-you-new-perspective-sequencing-experiment/ ...
written 14 months ago by achamess50
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Comment: C: RNA seq saturation analysis
... Are there are any scripts/tools that perform this analysis easily? I've looked and can't find anything off the shelf. ...
written 14 months ago by achamess50
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Answer: A: Pseudoreplication and comparing RNA-seq samples from the same animal
... >I'm not sure why you're including GFP+ cells in your comparison group, GFP+ vs. GFP- seems like a more reasonable comparison. The GFP cells make a considerable (~30%) of all the cells in the tissue. There are other types of cells too (non-neuronal). I was concerned that if I compared to GFP-, I ...
written 19 months ago by achamess50
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Pseudoreplication and comparing RNA-seq samples from the same animal
... Hi all, This is as much an experimental design question as a bioinformatic one, but it's something many of doing RNA-seq analysis deal with, so I thought I'd ask here. I'm looking to compare enrichment of genes in a GFP-labelled set of neurons in mouse. A colleague recommended that as the comparis ...
rna-seq written 19 months ago by achamess50
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Answer: A: Tool to append Illumina Read 1 to Read 2 for downstream demultiplexing
... Moving your answer here (with my modifications). join <(zcat AC1-10_S34_R1_001.fastq.gz | nl ) <(zcat AC1-10_S34_R2_001.fastq.gz|nl) | awk -F ' ' '{if ($2 ~ /^@NB501800/ ) {print $4" "$5;} else {print $2$3;}}' | gzip > new.fastq.gz Here is the output: ``` @NB501800:5:HKYVYAFXX:1: ...
written 2.4 years ago by achamess50
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Comment: C: Tool to append Illumina Read 1 to Read 2 for downstream demultiplexing
... It worked! Very nice. I need to spend more time learning the power of `awk`. Here is my update for for `.gz` input and output. I will probably now make some kind of loop to process all my files. Thank you! ...
written 2.4 years ago by achamess50
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Comment: C: Tool to append Illumina Read 1 to Read 2 for downstream demultiplexing
... Thanks. I'll give it a try. But can I use .fastq.gz? Sorry, I'm not a Unix pro, so this is my attempt: `join <(nl gzip -cd |cat AC1-10_S34_R1_001.fastq.gz) <(nl gzip -cd |cat AC1-10_S34_R2_001.fastq.gz) | awk -F ' ' '{if (@machineID ) {print $4" "$5;} else {print $2$3;}}' > new.fastq` ...
written 2.4 years ago by achamess50
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Comment: C: Tool to append Illumina Read 1 to Read 2 for downstream demultiplexing
... Hi. Thanks for the reply. R2 header. ...
written 2.4 years ago by achamess50

Latest awards to achamess

Popular Question 12 months ago, created a question with more than 1,000 views. For Ensembl GTF for Mouse that includes intron, exons, utrs, etc.
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Tool to append Illumina Read 1 to Read 2 for downstream demultiplexing
Popular Question 2.4 years ago, created a question with more than 1,000 views. For How to find CpG island shore?
Scholar 2.4 years ago, created an answer that has been accepted. For A: Tool to append Illumina Read 1 to Read 2 for downstream demultiplexing
Popular Question 5.2 years ago, created a question with more than 1,000 views. For How to find CpG island shore?

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