-
Hi,
I was skimming through some of the code and other open issues on support for other library (cell barcode/umi) designs. It looks like there is code for supporting inDrop libraries, but I wasn't su…
-
Dear all,
I am currently testing Shannon on our RNA–Seq data (40 to 80 million paired–end Illumina reads with 150 bp length) and have experienced some weird inconsistencies especially in the time t…
-
I tried the program on PacBio hifi reads, which were for amplicon sequencing of some plant DNA samples, barcoded on both ends. The reason is that LIMA generated very simple report missing a lot of inf…
-
Hello!
We are interested in generating mouse transcriptomics data. I was wondering if there are any recommendations for the minimum number of reads to perform so that the data will be ideal to run t…
-
It turns out that our default RNA-seq pipeline happily analyzed IonTorrent or ABI data and produces seemingly reasonable data
[GSE67124](https://gemma.msl.ubc.ca/expressionExperiment/showExpression…
-
Hello! I am writing seeking help with primer removal in cutadapt. I have Paired-end sequences, sequenced with Illumina. Illumina's own software removes index and adapters that are not of interest to…
-
1. Mainly wondering if NTSM is suitable for low coverage NGSdata?
2. In other words, how much depth of NGSdata can it be applied to?
-
This issue is reported by @ginamawla. I am including Gina’s writing and visualizations here with some modifications for the issue.
#### What data file(s) does this issue pertain to?
Transcriptom…
-
hey,
I'm trying to RNAspades on paired Illumina reads which didn't align to my reference. and I'm getting the following error:
== Error == system call for: "['/apps/RH7U2/gnu/SPAdes/3.14.0/bin/spad…
-
library(SummarizedExperiment)
library(TCGAbiolinks)
library(dplyr)
query.exp