manifest

#Salmon.Quant
#Wed Mar 30 19:25:12 UTC 2022
JVMLevel=
LSID=urn\:lsid\:genepattern.org\:module.analysis\:00420\:0.10.0
author=Anthony S. Castanza;UCSD-MesirovLab
categories=rna-seq
commandLine=<libdir>salmon_quant.sh -r <Reads> -i <Transcriptome.Index> -l <Library.Type> -e <Sampling> -n <N.Sampling> -s <seqBias> -g <gcBias> -p <posBias> -t <Mimic.Bowtie> -o <Recover.Orphans> -h <Hard.Filter> -d <Allow.Dovetail> -q <Dump.EQ> -m <reduce.GC.Memory> -f <Range.Factorization> -c <Range.Factorization.Bins> -b <biasSpeedSamp> -a <biasSpeedSamp.Factor> -j <job.cpuCount>
cpuType=any
description=Perform transcript-level quantification of RNA-seq data using Salmon (version 1.8.0).<br>\n\nSee\: <a href\="https\://salmon.readthedocs.io/en/latest/salmon.html\#using-salmon" target\="_blank">The Salmon User Guide</a>\nfor detailed usage guidelines.
documentationUrl=
fileFormat=.quant.sf;.tar.gz;gz;sf
job.cpuCount=3
job.docker.image=genepattern/salmon-quant\:beta_1.8.0
job.memory=16Gb
job.walltime=
language=any
name=Salmon.Quant
os=any
p10_MODE=
p10_TYPE=TEXT
p10_default_value=false
p10_description=Perform orphan "rescue" for reads. That is, if mappings are discovered for only one end of a fragment, or if the mappings for the ends of the fragment don't fall on the same transcript, then this flag will cause salmon to look upstream or downstream of the discovered mapping (anchor) for a match for the opposite end of the given fragment.
p10_fileFormat=
p10_flag=-o
p10_name=Recover.Orphans
p10_numValues=1..1
p10_optional=
p10_prefix=
p10_prefix_when_specified=
p10_type=java.lang.String
p10_value=true\=TRUE;false\=FALSE
p11_MODE=
p11_TYPE=TEXT
p11_default_value=false
p11_description=Turns off soft filtering and range-factorized equivalence classes, and removes all but the equally highest scoring mappings from the equivalence class label for each fragment.
p11_fileFormat=
p11_flag=-h
p11_name=Hard.Filter
p11_numValues=1..1
p11_optional=
p11_prefix=
p11_prefix_when_specified=
p11_type=java.lang.String
p11_value=true\=TRUE;false\=FALSE
p12_MODE=
p12_TYPE=TEXT
p12_default_value=false
p12_description=Dovetailing mappings and alignments are considered discordant and discarded by default - this is the same behavior that is adopted by default in Bowtie2. If you wish to consider dovetailing mappings as concordant (the previous behavior), you can do so by setting Allow.Dovetail to true.
p12_fileFormat=
p12_flag=-d
p12_name=Allow.Dovetail
p12_numValues=1..1
p12_optional=
p12_prefix=
p12_prefix_when_specified=
p12_type=java.lang.String
p12_value=true\=TRUE;false\=FALSE
p13_MODE=
p13_TYPE=TEXT
p13_default_value=false
p13_description=Setting to TRUE will cause Salmon to write a file in the auxiliary directory called eq_classes.txt that contains the equivalence classes and corresponding counts that were computed during quasi-mapping.
p13_fileFormat=
p13_flag=-q
p13_name=Dump.EQ
p13_numValues=1..1
p13_optional=
p13_prefix=
p13_prefix_when_specified=
p13_type=java.lang.String
p13_value=true\=TRUE;false\=FALSE
p14_MODE=
p14_TYPE=TEXT
p14_default_value=false
p14_description=Used with gcBias. This option replaces the per-nucleotide GC count with a rank-select capable bit vector, reducing the memory overhead from 4-bytes per nucleotide to ~1.25 bits, while being only marginally slower).
p14_fileFormat=
p14_flag=-m
p14_name=reduce.GC.Memory
p14_numValues=1..1
p14_optional=
p14_prefix=
p14_prefix_when_specified=
p14_type=java.lang.String
p14_value=true\=TRUE;false\=FALSE
p15_MODE=
p15_TYPE=TEXT
p15_default_value=false
p15_description=Range-factorization allows using a data-driven likelihood factorization, which can improve quantification accuracy on certain classes of difficult transcripts.
p15_fileFormat=
p15_flag=-f
p15_name=Range.Factorization
p15_numValues=1..1
p15_optional=
p15_prefix=
p15_prefix_when_specified=
p15_type=java.lang.String
p15_value=true\=TRUE;false\=FALSE
p16_MODE=
p16_TYPE=Integer
p16_default_value=4
p16_description=Positive integer that determines fidelity of range factorization. The larger x, the closer the factorization to the un-factorized likelihood, but the larger the resulting number of equivalence classes. A value of 1 corresponds to salmon's traditional rich equivalence classes. We recommend 4 (default) as a reasonable parameter for this option (it is what was used in the range-factorization paper).\n<br>\nIgnored if Range.Factorization \= FALSE
p16_fileFormat=
p16_flag=-c
p16_name=Range.Factorization.Bins
p16_numValues=1..1
p16_optional=
p16_prefix=
p16_prefix_when_specified=
p16_range=1+
p16_type=java.lang.Integer
p16_value=
p17_MODE=
p17_TYPE=TEXT
p17_default_value=false
p17_description=When evaluating the bias models (the GC-fragment model specifically), Salmon must consider the probability of generating a fragment of every possible length (with a non-trivial probability) from every position on every transcript. This results in a process that is quadratic in the length of the transcriptome. Setting biasSpeedSamp allows Salmon to consider only every ith fragment length and interploate the intermediate results speeding up this process by a multiplicative factor.
p17_fileFormat=
p17_flag=-b
p17_name=biasSpeedSamp
p17_numValues=1..1
p17_optional=
p17_prefix=
p17_prefix_when_specified=
p17_type=java.lang.String
p17_value=true\=TRUE;false\=FALSE
p18_MODE=
p18_TYPE=Integer
p18_default_value=5
p18_description=Set the sampling factor for biasSpeedSamp. Larger values speed up effective length correction, but may decrease the fidelity of bias modeling. However, reasonably small values (e.g. 10 or less) should have only a minor effect on the computed effective lengths, and can considerably speed up effective length correction on large transcriptomes. The default value for --biasSpeedSamp is 5.<br>\nIgnored if biasSpeedSamp \= FALSE
p18_fileFormat=
p18_flag=-a
p18_name=biasSpeedSamp.Factor
p18_numValues=1..1
p18_optional=
p18_prefix=
p18_prefix_when_specified=
p18_type=java.lang.Integer
p18_value=
p1_MODE=IN
p1_TYPE=FILE
p1_default_value=
p1_description=RNA-seq Reads.<br>\n<br>Paired-end reads must be gzipped and named as follows\:<br>\nRead 1\: SampleID_R1.fastq.gz, SampleID_1.fastq.gz, SampleID_R1.fq.gz, or SampleID_1.fq.gz<br>\nRead 2\: SampleID_R2.fastq.gz, SampleID_2.fastq.gz, SampleID_R2.fq.gz, or SampleID_2.fq.gz<br>\nWhere "SampleID" is the same string for both members of each pair.<br>\n<br>\nSingle-end reads must not have a _R1/_1 or _R2/_2 suffix before the .fq.gz/.fastq.gz file extension.<br><br>\n<b>Warning\:</b> Splitting reads for a single sample across multiple files (eg\: SampleA_R1_001.fq.gz, SampleA_R1_002.fq.gz; SampleA_R2_001.fq.gz, SampleA_R2_002.fq.gz;) is not supported.
p1_fileFormat=.fastq.gz;.fq.gz;fastq.gz;fq.gz
p1_flag=-r
p1_name=Reads
p1_numValues=1+
p1_optional=
p1_prefix=
p1_prefix_when_specified=
p1_type=java.io.File
p1_value=
p2_MODE=IN
p2_TYPE=FILE
p2_choices=https\://datasets.genepattern.org/data/module_support_files/Salmon.Quant/gencode.v39.annotation.k31.salmon_full_decoy_index.tar.gz\=Human_Gencode_v39_Kmer31_Full_Decoy;https\://datasets-genepattern-org.s3.amazonaws.com/data/test_data/Salmon/gencode.v37.annotation.k31.salmon_full_decoy_index.tar.gz\=Human_Gencode_v37_Kmer31_Full_Decoy_Index;https\://datasets.genepattern.org/data/module_support_files/Salmon.Quant/gencode.vM28.annotation.k31.salmon_full_decoy_index.tar.gz\=Mouse_Gencode_vM28_Kmer31_Full_Decoy;https\://datasets-genepattern-org.s3.amazonaws.com/data/test_data/Salmon/gencode.vM26.annotation.k31.salmon_full_decoy_index.tar.gz\=Mouse_Gencode_vM26_Kmer31_Full_Decoy_Index
p2_default_value=https\://datasets.genepattern.org/data/module_support_files/Salmon.Quant/gencode.v39.annotation.k31.salmon_full_decoy_index.tar.gz
p2_description=An Indexed transcriptome created with `Salmon Indexer`.<br>\nMust be in .tar.gz format.
p2_fileFormat=.tar.gz;tar.gz
p2_flag=-i
p2_name=Transcriptome.Index
p2_numValues=1..1
p2_optional=
p2_prefix=
p2_prefix_when_specified=
p2_type=java.io.File
p2_value=
p3_MODE=
p3_TYPE=TEXT
p3_default_value=A
p3_description=The library type of the RNA-seq. This describes the relative orientation of the reads. (Default\: automatic inference of library type)\n<br><br>\nCommon Salmon options are described in contrast with equivalent options from other quantification tools.\n<style type\="text/css">\n.tg  {border-collapse\:collapse;border-spacing\:0;}\n.tg td{border-color\:black;border-style\:solid;border-width\:1px;font-family\:Arial, sans-serif;font-size\:12px;}\n.tg th{border-color\:black;border-style\:solid;border-width\:1px;font-family\:Arial, sans-serif;font-size\:12px;\n  font-weight\:normal;}\n.tg .tg-0pky{border-color\:inherit;text-align\:left;vertical-align\:top}\n</style>\n<table class\="tg">\n<tbody>\n  <tr>\n    <th class\="tg-0pky">RSeQC Result (Majority of Reads)</th>\n    <th class\="tg-0pky">No clear majority</th>\n    <th class\="tg-0pky">1++,1--,2+-,2-+</th>\n    <th class\="tg-0pky">1+-,1-+,2++,2--</th>\n  </tr>\n  <tr>\n    <td class\="tg-0pky">Salmon / Sailfish</td>\n    <td class\="tg-0pky">IU</td>\n    <td class\="tg-0pky">ISF</td>\n    <td class\="tg-0pky">ISR</td>\n  </tr>\n  <tr>\n    <td class\="tg-0pky">TopHat / Cufflinks</td>\n    <td class\="tg-0pky">library-type fr-unstranded</td>\n    <td class\="tg-0pky">library-type fr-secondstrand</td>\n    <td class\="tg-0pky">library-type fr-firststrand</td>\n  </tr>\n  <tr>\n    <td class\="tg-0pky">HISAT2</td>\n    <td class\="tg-0pky">default</td>\n    <td class\="tg-0pky">--rna-strandedness FR</td>\n    <td class\="tg-0pky">-rna-strandedness RF</td>\n  </tr>\n  <tr>\n    <td class\="tg-0pky">HTSeq</td>\n    <td class\="tg-0pky">stranded --no</td>\n    <td class\="tg-0pky">stranded --yes</td>\n    <td class\="tg-0pky">stranded --reverse</td>\n  </tr>\n</tbody>\n</table>\n\nSee also\: https\://salmon.readthedocs.io/en/latest/salmon.html\#what-s-this-libtype
p3_fileFormat=
p3_flag=-l
p3_name=Library.Type
p3_numValues=1..1
p3_optional=
p3_prefix=
p3_prefix_when_specified=
p3_type=java.lang.String
p3_value=A\=Automatic Detection;ISF\=ISF (Inward, read 1 from the forward strand);ISR\=ISR (Inward, read 1 from the reverse strand);IU\=IU (Inward, Unstranded);OSF\=OSF (Outward, read 1 from the forward strand);OSR\=OSR (Outward, read 1 from the reverse strand);OU\=OU (Outward, Unstranded);SF\=SF (Single-End, read 1 from the forward strand);SR\=SR (Single-End, read 1 from the reverse strand);U\=U (Single-End, Unstranded)
p4_MODE=
p4_TYPE=TEXT
p4_default_value=BOOT
p4_description=Sampling method for assessing technical variance, used for downstream differential gene/transcript expression analysis with Sleuth (not needed for DESeq2).\n<br><br>\nMethods available\:<br> <b>None</b> - skips technical variance estimation<br>\n<b>Bootstraps</b> (Recommended) (bootstrapped abundance estimates) - resampling (with replacement) from the counts assigned to the fragment equivalence classes, and then re-running the optimization procedure for each such sample.<br>\n<b>GibbsSamples</b> - samples are generated using posterior Gibbs sampling over the fragment equivalence classes rather than bootstrapping.
p4_fileFormat=
p4_flag=-e
p4_name=Sampling
p4_numValues=1..1
p4_optional=
p4_prefix=
p4_prefix_when_specified=
p4_type=java.lang.String
p4_value=NA\=None;BOOT\=Bootstraps;GIBB\=GibbsSamples
p5_MODE=
p5_TYPE=TEXT
p5_default_value=true
p5_description=Salmon will learn and correct for sequence-specific biases in the input data. Specifically, this model will attempt to correct for random hexamer priming bias.
p5_fileFormat=
p5_flag=-s
p5_name=seqBias
p5_numValues=1..1
p5_optional=
p5_prefix=
p5_prefix_when_specified=
p5_type=java.lang.String
p5_value=true\=TRUE;false\=FALSE
p6_MODE=
p6_TYPE=TEXT
p6_default_value=true
p6_description=Salmon learn and correct for fragment-level GC biases in the input data. Specifically, this model will attempt to correct for biases in how likely a sequence is to be observed based on its internal GC content.
p6_fileFormat=
p6_flag=-g
p6_name=gcBias
p6_numValues=1..1
p6_optional=
p6_prefix=
p6_prefix_when_specified=
p6_type=java.lang.String
p6_value=true\=TRUE;false\=FALSE
p7_MODE=
p7_TYPE=TEXT
p7_default_value=true
p7_description=Salmon will construct a model of a position-specific fragment start distribution. This is meant to model non-uniform coverage biases that are sometimes present in RNA-seq data (e.g. 5' or 3' positional bias).
p7_fileFormat=
p7_flag=-p
p7_name=posBias
p7_numValues=1..1
p7_optional=
p7_prefix=
p7_prefix_when_specified=
p7_type=java.lang.String
p7_value=true\=TRUE;false\=FALSE
p8_MODE=
p8_TYPE=Integer
p8_default_value=30
p8_description=The number of bootstrapped estimates/Gibbs samples used for technical variance estimation
p8_fileFormat=
p8_flag=-n
p8_name=N.Sampling
p8_numValues=1..1
p8_optional=
p8_prefix=
p8_prefix_when_specified=
p8_type=java.lang.Integer
p8_value=
p9_MODE=
p9_TYPE=TEXT
p9_default_value=off
p9_description=Sets the parameters related to mapping and selective alignment to mimic alignment using Bowtie2.\n<br>\noff\: default\n<br>\nmimicBT2\: mimic alignment using Bowtie2 (with the flags --no-discordant and --no-mixed), but using the default scoring scheme and allowing both mismatches and indels in alignments.\n<br>\nmimicStrictBT2\: mimic alignment using Bowtie2 (with the flags suggested by RSEM), but using the default scoring scheme and allowing both mismatches and indels in alignments. These setting essentially disallow indels in the resulting alignments.
p9_fileFormat=
p9_flag=-t
p9_name=Mimic.Bowtie
p9_numValues=1..1
p9_optional=
p9_prefix=
p9_prefix_when_specified=
p9_type=java.lang.String
p9_value=off\=off;BT2\=mimicBT2;Strict\=mimicStrictBT2
privacy=public
publicationDate=11/17/2021 10\:52 
quality=preproduction
src.repo=https\://github.com/genepattern/Salmon.Quant/tree/v0.10
taskDoc=Salmon.Quant.pdf
taskType=rna-seq
userid=acastanza
version=Update to Salmon v1.8.0