learning-MD

Hi, wanted to follow-up on this, as I have several hashed samples that I'd like to use velocyto for. Any chance you figured this out, @carbycrab, or anyone else have...

Thanks! Yes, there are feature barcodes to identify what corresponds to what sample. I think I'll just have to run one hashed sample to see how it works out and...

Sorry for the delay - this is what pops up: ``` WARNING: failed to set O_CLOEXEC flags on image WARNING: failed to set O_CLOEXEC flags on image ERROR : Failed...

Thanks @mourisl! We had targeted 50,000 reads per cell for the gene expression libraries and 5,000 reads per cell for the feature barcode libraries. I would think that that should...

Thanks @mourisl - it's single-cell RNA-seq. We did not do nucleus-sequencing. If it helps, it wasn't the Multiome kit (that's the snRNA- + snATAC-seq combo). We just added hashtag oligos...

Sorry for the delay. Below is what I see: `~$ samtools view samples.bam | head -n 5` `A01177:64:HTJ7KDSX3:2:1407:4282:35900 163 chr1 10189 255 12S64M169913N75M = 180283 170206 CCTAACCCTAACCCCTAACCCTAATCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAAACCCTAACCCAAAAACCCTAACCATAACCCTAACCCTAACCCTAAACCTAACCCTAATCCTTACCCTTACCCTAACC FFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFF,FF,FFFFFFFFFFFFF:FFFFFFF::FFFF,FFFFF,FFFFFFF,FF:,F,FFFF::F:FFFFF,F:FFFF,FFFFF,:F,::,F,F:,,F,:F,:,,F:,::F,FF,FFF,,,F:F NH:i:1 HI:i:1...

I really do think it's a gene expression QC thing - for example, if I merge the airr_report file with my Seurat object with minimal filtering (before filtering nFeatures/nCounts and...

Thanks again for all your help @mourisl. One question I had, as I'm using the data as input to scRepertoire: as I'm running the barcoderep-to-10X.pl, I'm getting the following error:...

I'm an idiot. I just needed to give myself permission to access the barcode_report.tsv file. Thanks!

To continue the same thread with a question, the following error popped up with one of my bam files while the rest of the bam files worked without any issue:...