Tom Kelly

I've seen a few alternative examples using the structure of the SWC content, such as @BillMills doing one where learners created a `thesis` repo and edited `abstract`, `methods`, and `results`...

Sorry our server got shutdown for maintenance (while I was on leave) so I can't access the docker container where I tested this version. I'm trying to get it back...

I get a similar error running DropSeq data (Mascosko 2015). I downloaded files from GEO and SRA and did some filtering. SRR1873277_S1_L001_R1_001.fastq ``` @AH2HM7BGXX:1:11101:10007:10911 TAACGTACAGGAGGAGTACG +AH2HM7BGXX:1:11101:10007:10911 AA7AAFAFFFAFFFFFAAAF @AH2HM7BGXX:1:11101:10008:15270 GCATGAAACTTCCACGGGCC +AH2HM7BGXX:1:11101:10008:15270...

In my case, I was able to fix it by adding the second field to the header. ``` sed -i "1~4s/$/ 1:N:0:0/g" SRR1873277_S1_L001_R[12]_001.fastq ``` With this `get_cell_whitelist`, `extend_barcode_top`, and `repair_barcodes`...

@terooatt and I are in the same lab, we're running the pipeline on the same Debian server. I think this was the same issue I had so it is safe...

I've written a sed solution to extract the barcodes and UMI from R1. This will return a Read1 with an 18bp barcode and 8bp UMI. ``` Read1s=("Sample_S1_L001_R1_001.fastq" "Sample_S1_L002_R1_001.fastq") Read2s=("Sample_S1_L001_R2_001.fastq" "Sample_S1_L002_R2_001.fastq")...

As discussed here: https://github.com/nf-core/demultiplex/issues/14 https://github.com/nf-core/scrnaseq/issues/31#issuecomment-655556492 Part of this milestone https://github.com/nf-core/demultiplex/milestone/2 I note there is an existing module submissed by @Emiller88 (https://github.com/nf-core/modules/pull/979) for Cell Ranger with similar functionality. This should serve...

This tool has now been accepted at a peer-reviewed journal. We have also developed a graphical user application during revisions: https://genomec.gsc.riken.jp/gerg/UniverSC/ I prepared a module from the templates and updated...

I'll share updates to the UniverSC module for feedback. It still needs tests but inputs and documentation have been updated. Note this module requires a docker container and a conda...

Hi @JoseEspinosa thanks for letting me know. I'm ok to mark it as Draft/WIP as it is but it is almost ready to review I think. What is the timeframe...