Thank you for freely providing these datasets and analysis scripts.
I've tried to recover the gene expression and antibody features data from an original 10X bam file (sample GSM4138874) and even though I could get the the gene expression data from this file, I can't recover the antibody features reads from the raw 10X bam files.
I've tried extracting the reads using the following one liner:
samtools view original10X.bam | LC_ALL=C grep -F fb:Z | samtools view -b -o original10X_ADT.bam
The one liner is from an official 10X Genomics support page: https://kb.10xgenomics.com/hc/en-us/articles/360022448251-Is-there-way-to-filter-the-BAM-file-produced-by-10x-pipelines-with-a-list-of-barcodes-
It did not generate any output and at a read inspection I could not find reads with the fb:Z flag that is used to mark reads pertaining the antibody features.
Has anyone encountered the same issue when they tried to retrieve antibody features data from in raw 10x Bam Files from this publication? Thank you for your help!
Thank you for freely providing these datasets and analysis scripts.
I've tried to recover the gene expression and antibody features data from an original 10X bam file (sample GSM4138874) and even though I could get the the gene expression data from this file, I can't recover the antibody features reads from the raw 10X bam files.
I've tried extracting the reads using the following one liner:
samtools view original10X.bam | LC_ALL=C grep -F fb:Z | samtools view -b -o original10X_ADT.bam
The one liner is from an official 10X Genomics support page: https://kb.10xgenomics.com/hc/en-us/articles/360022448251-Is-there-way-to-filter-the-BAM-file-produced-by-10x-pipelines-with-a-list-of-barcodes-
It did not generate any output and at a read inspection I could not find reads with the fb:Z flag that is used to mark reads pertaining the antibody features.
Has anyone encountered the same issue when they tried to retrieve antibody features data from in raw 10x Bam Files from this publication? Thank you for your help!