GreenleafLab
Antibody features in raw 10x Bam Files provided in the repository link
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!
Hi! I was having the same problem accessing this particular dataset. For the PBMC and whole Bone Marrow CITEseq datasets both libraries are present after running bamtofastq, but both CD34 enriched datasets seem to only contains information about gene expression (samtools view -H bamfile; no Antibody Capture information is present):
Whole Bone Marrow library samtools view -H:
CO 10x_bam_to_fastq:I1(BC:QT) CO 10x_bam_to_fastq:R1(CR:CY,UR:UY) CO 10x_bam_to_fastq:R2(SEQ:QUAL) CO library_info:{"library_id":"0","library_type":"Antibody Capture","gem_group":1} CO library_info:{"library_id":"1","library_type":"Gene Expression","gem_group":1}
CD34 enriched library samtools view -H:
CO 10x_bam_to_fastq:I1(BC:QT) CO 10x_bam_to_fastq:R1(CR:CY,UR:UY) CO 10x_bam_to_fastq:R2(SEQ:QUAL) CO library_info:{"library_id":"0","library_type":"Gene Expression","gem_group":1} CO user command line: STAR --genomeDir /oak/stanford/groups/wjg/klemm/resources/10x/genomes/refdata-cellranger-hg19-3.0.0/star --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within KeepPairs --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:PCD34_R6:0:1:HLCHWBGX9:1 SM:PCD34_R6 LB:0.1 PU:PCD34_R6:0:1:HLCHWBGX9:1 PL:ILLUMINA --readFilesIn /dev/fd/63
I was wondering whether you managed to access this information in the end.
Thank you in advance
