I'm very happy to announce that MultiQC v1.15 was just released! 🎉

https://github.com/ewels/MultiQC/releases/tag/v1.15

It comes with 🐛 fixes for #10xGenomics #CellRanger fix, #mosdepth tweaks, and supports a new tool #Librarian to predict library type from FastQ base composition 🕵🏻‍♂️ 🧬plus much more!

Also included is a ~5-7 fold speed-up in the initial file search. This will shave off a chunk of run-time off for people generating big reports 🏎💨

Thanks to Vlad Savelyev for this with a hat tip to Pontus Höjer at the end 🙏🏻

Split a #BAM file produced by #CellRanger into one file per #singlecell barcode, using #samtools and #awk:

samtools view in.bam | awk '/CB:Z:/{f=substr($0,match($0,/CB:Z:[ACGT]{16}/)+5,16)".txt"}{print>>f}'

#cellranger #scRNA-seq #Seurat #bioinformatics

I know there are Lane 004 and Lane 005 for FA1_S4 and FA2_S5 respectively, Lane001 ~ Lane 00
for FA1_S1 and FA2_S2. So How do I get the count matrix by #cellranger for FA1 and FA2 as two datasets not a file for each fastq file?

Any suggestion will be appreciated!