FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022

Issues

• Visium fastqs clarification

  #20 opened 8 months ago by trus-uic
  1

• Downloaded INVADEseq data not work for cellranger

  #15 opened a year ago by oyxf
  5

• Sample name in `headneck_gex_16s_mix_dedup.csv`

  #17 opened a year ago by tmaruy
  5

• detection of microbial reads on 10X Visium slides

  #19 opened a year ago by ftencaten
  0

• error for gatk PathSeqPipelineSpark "java: bwa.c:329: bwa_mem2idx: Assertion `k == l_mem' failed."

  #18 opened a year ago by leogg738
  1

• Running for Part2. 10X single cell data

  #16 opened a year ago by hibiscuslee
  1

• Visium QC filtering - Mitochondrial content

  #14 opened a year ago by cathalgking
  1

• Running for Part1.10x Visium spatial transcriptomic data

  #13 opened 2 years ago by februaryfang
  3

• File info

  #12 opened 2 years ago by AnnaAntonatouPap
  12

• Doubts about the SRA ID

  #11 opened 2 years ago by februaryfang
  4

• pathseq bam is missing reads in the literature

  #10 opened 2 years ago by jr-ran
  11

• Requestion about Coordinate Information

  #9 opened 2 years ago by yunbokai
  1

• Running for Part2. 10X single cell data

  #8 opened 2 years ago by ChoiJi-Hye
  1

• Running pipeline for non-Visium data

  #7 opened 2 years ago by AnnaAntonatouPap
  3

• Availability of Seurat objs

  #6 opened 2 years ago by MathiniVaikunthan
  1

• GATK pathseq

  #4 opened 2 years ago by zhangshuyue1
  1

• GATK pathseq

  #5 opened 2 years ago by zhangshuyue1
  1

• The spatial coordinates of 10X Visium samples

  #3 opened 2 years ago by jiwoongbio
  1

• cannot find my_sample.visium.raw_matrix.genus.csv

  #2 opened 2 years ago by NicolaasVanRenne
  11

• A issue in validate_and_count.py

  #1 opened 2 years ago by TequilaSunrise84
  6