CombinedAlignment: Title

In inDAGO: A GUI for Dual and Bulk RNA-Sequencing Analysis

Title

Description

Title

Usage

CombinedAlignment(
  lalista,
  nodes,
  readsPath,
  GenomeConcIndex,
  outBam,
  threads,
  outFormat,
  phredScore,
  maxExtractedSubreads,
  consensusVote,
  mismatchMax,
  uniqueOnly,
  maxMultiMapped,
  indelLength,
  fragmentMinLength,
  fragmentMaxLength,
  matesOrientation,
  readOrderConserved,
  coordinatesSorting,
  allJunctions,
  tempfolder,
  readsAlignedBlock
)

Arguments

lalista	list of samples
nodes	logic cores
readsPath	sample folders
GenomeConcIndex	genome index
outBam	output folder
threads	processes
outFormat	BAM or SAM
phredScore	quality score
maxExtractedSubreads	number of subreads
consensusVote	consensus
mismatchMax	mismatch
uniqueOnly	no multimapping
maxMultiMapped	multimapping
indelLength	indel
fragmentMinLength	fragment minumum length
fragmentMaxLength	fragment maximum length
matesOrientation	mate orientation
readOrderConserved	read order
coordinatesSorting	sorting
allJunctions	junctions
tempfolder	temporary folder
readsAlignedBlock	chunks

inDAGO documentation built on Aug. 8, 2025, 7:47 p.m.