FelixKrueger/SNPsplit

Issues

• Question about allele_flagged.bam and genome1.bam/genome2.bam files

  #82 opened 8 months ago by xixueyu96
  2

• trouble with BS-Seq

  #80 opened 8 months ago by lucacozzuto
  9

• Genome preparation:129S1 (paternal) mice × B6D2F1/J (F1 of C57BL6NJ × DBA2J, maternal) mice

  #71 opened 2 years ago by lelesama
  7

• About singletons

  #81 opened 8 months ago by ddepierre
  1

• minimap2

  #70 opened 2 years ago by kullrich
  4

• Question about assigning 'unassignable' reads

  #79 opened 10 months ago by RobertBaird
  2

• Getting 0 reads processed

  #74 opened 2 years ago by yonniejon
  11

• How to define high-confidence SNPs?

  #78 opened a year ago by Ulixmanna
  1

• Zero segregation for scRNAseq

  #77 opened 2 years ago by GangLiTarheel
  5

• Bowtie1 as the aligner of Bismark

  #76 opened 2 years ago by lelesama
  1

• Update SNPsplit to v8 release of the Mouse Genomes Project

  #72 opened 2 years ago by FelixKrueger
  2

• Tutorial for SNPsplit

  #73 opened 2 years ago by yonniejon
  2

• SNP level counting showing bi and mono allele count for same gene

  #68 opened 2 years ago by luckysardar
  2

• Mask reference genome for human genome build 37 using bisulphite fasta file

  #65 opened 2 years ago by nmfad
  6

• Why I can't split bisulfite data ?

  #64 opened 2 years ago by chaoyang666
  3

• Using SNPsplit for single cell data

  #69 opened 2 years ago by taolincj
  4

• high reads did not contain one of the expected bases at known SNP positions

  #67 opened 2 years ago by ChenfuShi
  7

• single end mode not working

  #66 opened 2 years ago by rberrens
  2

• SNPsplit for mouse RNA-seq data

  #59 opened 3 years ago by Lu-103
  8

• How to phase Hi-C data using SNPs

  #63 opened 3 years ago by hmyh1202
  2

• N-masking human genome

  #62 opened 3 years ago by parichitran
  2

• single-end mode does not work

  #61 opened 3 years ago by shanwai1234
  2

• 0-indexed or 1-indexed for the SNP output?

  #60 opened 3 years ago by sshen82
  2

• Using SNPsplit to analysis Bisulfite-Seq data in plant

  #58 opened 3 years ago by GatorShan
  2

• Two much variation in the Two strain specific reads percentage

  #57 opened 3 years ago by luckysardar
  1

• Running SNPsplit in parallel

  #50 opened 3 years ago by Grishnahk
  3

• Nmasked human genome

  #55 opened 3 years ago by fanghe0720
  1

• Which reference genome I have to use it for genomepreparation

  #54 opened 3 years ago by luckysardar
  7

• SNP split for the hybrid cross two different strains

  #53 opened 3 years ago by Hemantcnaik
  9

• Error with SNPsplit_genome_preparation

  #52 opened 3 years ago by jprippe
  2

• Using the --full_sequence genome

  #51 opened 3 years ago by ezecalvo
  2

• How to use the SNPsplit for higher version of VCF

  #44 opened 3 years ago by Hemantcnaik
  11

• Some questions about working on plant species

  #45 opened 3 years ago by CrazyHsu
  2

• Question about genome preparation for C57BL/6J x JF1/Ms hybrid mouse

  #41 opened 3 years ago by pplaw
  11

• Why all my reads are unassigned

  #49 opened 4 years ago by skelviper
  2

• SNPsplit_genome_preparation processing error on custom vcf and genome

  #47 opened 4 years ago by wwang-chcn
  5

• BS-seq about SNP_split

  #43 opened 4 years ago by zhangaicen
  3

• Look at file type auto-detection

  #42 opened 4 years ago by FelixKrueger
  1

• SNP removal in Bismark

  #40 opened 4 years ago by pubudumanoj
  1

• prepareGenome

  #38 opened 4 years ago by nservant
  6

• C>T SNPs preventing the assignment

  #33 opened 4 years ago by GuidoBarzaghi
  3

• Output genome files contain UA flags

  #32 opened 4 years ago by GuidoBarzaghi
  2

• 'S' CIGAR operation not allowed

  #36 opened 4 years ago by brainfo
  4

• Supporting soft-clipping

  #28 opened 4 years ago by Shians
  5

• PrepareGenome input

  #39 opened 5 years ago by nservant
  2

• Add option to skip sorting

  #37 opened 5 years ago by FelixKrueger
  0

• SNP value column in input snp file correspond to which information in vcf format files?

  #35 opened 5 years ago by brainfo
  1

• STAR provides only unassigned reads

  #34 opened 5 years ago by yeroslaviz
  22

• Question about analysis pipeline when using SNPsplit

  #31 opened 5 years ago by AIBio
  8

• Stats in YAML format to enable integration into MultiQC

  #29 opened 5 years ago by FelixKrueger
  2