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[plt2,SeqMapp] demultiplex mix 10xRNA-ATAC #458

Closed biomystery closed 4 years ago

biomystery commented 4 years ago

http://epigenomics.sdsc.edu:8000/nextseq/262/

biomystery commented 4 years ago 
Read Length:         50+8+16+93
Location:            /projects/ps-epigen/nextSeq/200625_NB501692_0014_AHYCFTAFXY
MM_346  SI-NA-C2
MM_347  SI-NA-C3
MM_348  SI-NA-C4
MM_349  SI-NA-C5
MM_350  SI-NA-C6
MM_351  SI-NA-C7
MM_352  SI-NA-C8
MM_353  SI-NA-C9
MM_354  SI-GA-A1
MM_355  SI-GA-A2
MM_356  SI-GA-A3
MM_357  SI-GA-A4
MM_358  SI-GA-A5
MM_359  SI-GA-A6
MM_360  SI-GA-A7
MM_361  SI-GA-A8 (edite
biomystery commented 4 years ago

for RNA: demultiplex bcl2fastq --run 200605_NB501692_0012_AHCCWNAFX2 --use-bases-mask Y28n,I8,N16,Y91n -p 16 --sample-sheet samplesheet_6.csv --output-dir /mnt/silencer2/home/spreissl/ --no-lane-splitting --create-fastq-for-index-reads rename: mv SI-GA-F9_3/JB_235_2_S3_I1_001.fastq.gz SI-GA-F9_3/JB_235_2_S3_L001_I1_001.fastq.gz cellranger count: cellranger count --id=BPD_D170 --transcriptome /projects/ps-epigen/GENOME/hg38/10x_Genomics3.0/refdata-transcripts --fastqs /projects/ps-epigen/platform2_outputs/spreissl/Chromium_20200617 --sample=BPD_D170 --expect-cells=7000 --chemistry=SC3Pv3 --localcores=8 --localmem=32 samplesheet_6.csv [Header] EMFileVersion,4 [Reads] 28 Click to expand inline (89 lines)

4:18 For ATAC: demultiplex: cellranger-atac-1.2.0/cellranger-atac mkfastq --run 200604_NB501692_0011_AH73GFBGXF --csv samplesheet_4.csv run cellranger count with regular settings samplesheet_4.csv Lane,Sample,Index *,JB_235_2,SI-NA-C1

4:18 Hi Frank this is what I did for previous samples for mixed libraries 4:19 does that make sense? 4:20 https://kb.10xgenomics.com/hc/en-us/articles/115003082371-How-to-demultiplex-a-dual-indexed-flowcell- 10X Genomics10X Genomics How to demultiplex a dual indexed flowcell? Question: How can I demultiplex a dual-indexed flowcell? Answer: Please note that Single Cell 3' libraries, Single Cell 5' libraries, and Genome libraries are single-indexed. We do not recommend to... 4:20 note: the "N" as flag for demultiplexing of RNA portion of the run

biomystery commented 4 years ago

https://github.com/epigen-UCSD/epigen_ucsd_django/commit/dc5a90dcec8e80ed3d7e1550121cbf12ebb19be1