nunofonseca/irap

Issues

• Configuration file for strand specific protocol

  #108 opened 3 years ago by lissur
  0

• iRAP pipeline for EMBL-EBI Expression Atlas

  #107 opened 5 years ago by lissur
  1

• sample name do not match

  #102 opened 6 years ago by sb43
  0

• Downloads to a submodule?

  #106 opened 6 years ago by pinin4fjords
  0

• fastq_pre_barcodes.c:34:17: fatal error: bam.h: No such file or directory

  #104 opened 6 years ago by jianglinghan
  0

• aux/R/irap_de.R::process.cmdline.args mis-casts --min (opt$min_count) as a string, should be integer

  #101 opened 6 years ago by vviyer
  1

• docker image for v1.0.1

  #96 opened 6 years ago by kathryn-beal
  2

• No rule to make target

  #99 opened 6 years ago by sb43
  1

• docker image 1.0.1 not working

  #98 opened 6 years ago by sb43
  1

• iRAP does not recognise stage0 completion for large genomes with HISAT2

  #87 opened 6 years ago by pinin4fjords
  5

• sh: 1: set: Illegal option -o pipefail error in "irap_gtf_to_fasta".

  #77 opened 6 years ago by shrho
  4

• Error running Docker image

  #60 opened 6 years ago by larsgtoicr
  2

• missing file on R component

  #32 opened 6 years ago by PeteClapham
  5

• irap_raw2metric no html file, not gzipped

  #50 opened 6 years ago by freekvh
  7

• failed to load GTF file

  #53 opened 6 years ago by byb121
  3

• our_prefix error when analysis name is same as the raw read file name without suffix

  #52 opened 6 years ago by byb121
  2

• iRAP's Kallisto call seems to provide read length at fragment size parameter

  #67 opened 6 years ago by pinin4fjords
  1

• RSEM strandness

  #54 opened 7 years ago by r-panero
  12

• Docker link in wiki is wrong

  #59 opened 7 years ago by larsgtoicr
  1

• TPM values rounded to 2 decimals

  #55 opened 7 years ago by freekvh
  3

• Set to 85% of the read by default

  #25 opened 7 years ago by freekvh
  13

• Not handling 'qual_filtering=none' as expected

  #48 opened 7 years ago by byb121
  1

• mapper options in config file is ignored

  #49 opened 7 years ago by byb121
  3

• Quantify the amount of rRNA in a library/sequencing experiment

  #39 opened 7 years ago by freekvh
  3

• contamination genomes built with bowtie2 won't be recognised in contamination filtering

  #47 opened 7 years ago by byb121
  1

• Contamination check errors

  #38 opened 7 years ago by freekvh
  4

• bamToFastq pickup the wrong bam file name

  #41 opened 7 years ago by byb121
  2

• file existence check

  #43 opened 7 years ago by byb121
  1

• gnpplot

  #27 opened 7 years ago by jodyphelan
  3

• compress FastQ?

  #46 opened 7 years ago by byb121
  1

• bamToFastq produces overwhelming warnings due to secondary alignments

  #45 opened 7 years ago by byb121
  1

• No rule to make target

  #40 opened 7 years ago by jodyphelan
  3

• -R is ignored when R is not preinstalled

  #42 opened 7 years ago by byb121
  1

• Merging Matrices in libTSVAggrTransByGene fails?

  #36 opened 7 years ago by Niklas123Niklas
  20

• how to norm the multiple bio replication TPM values into one tissue/condition value?

  #37 opened 7 years ago by wangyugui
  2

• more guideline for Atlas SOP

  #35 opened 7 years ago by wangyugui
  2

• Problem with Report generation

  #33 opened 7 years ago by Niklas123Niklas
  10

• Why the "samtools view -F 4" and the split of tsv files

  #34 opened 7 years ago by freekvh
  2

• Could pre-compiled binaries by considered as part of an installation method ?

  #30 opened 7 years ago by PeteClapham
  4

• Add to Dockstore with CLW mapping

  #31 opened 8 years ago by keiranmraine
  1

• Strandedness setting in iRAP conf

  #29 opened 8 years ago by freekvh
  2

• IGV_VERSION=2.1.24

  #23 opened 8 years ago by freekvh
  3

• make: *** No rule to make target '

  #28 opened 8 years ago by jodyphelan
  11

• Unknown regexp modifier "/t" at (eval 1) line 1, at end of line

  #26 opened 8 years ago by jodyphelan
  4

• Bug?

  #24 opened 8 years ago by Niklas123Niklas
  8

• Problem dry-running the ecoli_ex.conf file

  #22 opened 8 years ago by ikramu
  2

• No multithread for bowtie2-build

  #20 opened 8 years ago by Niklas123Niklas
  12

• VM errors

  #21 opened 8 years ago by freekvh
  4

• Error running irap_install.sh

  #19 opened 8 years ago by Niklas123Niklas
  5

• normalization of counts returns an error

  #18 opened 8 years ago by stkachev
  4