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comp-metadata/docs/quantification/transcriptome/SXPv2.xml

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pebert ADD: process files for transcriptome quant. - several issues, e.g., m…
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<?xml version="1.0"?>
<?xml-stylesheet type="text/css" href="http://deep.mpi-inf.mpg.de/DAC/files/style/deep_process_style.css"?>
<process>
<name>SXP</name>
<version>2</version>
<author>
<name>Filippos Klironomos</name>
<email>filippos.klironomos@mdc-berlin.de</email>
</author>
<description>
*) miRDeep2 pipeline involves:
*) mapping of reads to genome and keeping those uniquely mapped
*) extracting bracketing DNA of the uniquely mapped reads
*) RNAfold extracted sequences and keeping those that form unbifurcated hairpins
*) scoring putative precursors:
*) expect greater number of reads mapping to either the -5p or -3p strand and very little to the hairpin
*) short 3&apos; duplex overhang characteristic of Drosha/Dicer processing adds to the score
*) relative and absolute stabilities contribute to the score
*) if 5&apos; end of mature sequence is identical to that of known mature sequence it adds to the score
*) randomly permuting read signatures with putative precursor sequences in order to determine the FPR
Internally miRDeep2 uses the following packages:
RNAfold version 2.1.7
RANDFOLD version 2
</description>
<inputs>
<filetype>
<identifier>config</identifier>
<format>TSV</format>
<quantity>single</quantity>
<comment>
this is the configuration file that miRDeep2 uses to locate the FASTQ library and assign the 3-character identification to it
</comment>
</filetype>
</inputs>
<!-- Following section: list reference files [e.g. reference genomes] used in this process -->
<references>
<filetype>
<identifier>genome</identifier>
<format>fasta</format>
<quantity>single</quantity>
<comment>
<![CDATA[
hs37d5 and GRCm38mm10 genomes are modified as follows:
*) IDs are simplified, everything to the right of the first white space encountered is removed,
*) all ambiguously called nucleotides [URYSWKMBDHV] have been masked to 'N'.
The following script does all this:
sed -e 's/^>\(\S\+\)\s.*$/>\1/' -e '/^[^>]/s/[UuRrYySsWwKkMmBbDdHhVv]/N/g' hs37d5.fa > hs37d5_simple.fa
sed -e 's/^>\(\S\+\)\s.*$/>\1/' -e '/^[^>]/s/[UuRrYySsWwKkMmBbDdHhVv]/N/g' GRCm38mm10.fa > GRCm38mm10_simple.fa
]]>
</comment>
</filetype>
<filetype>
<identifier>genome_index</identifier>
<format>bowtie-index</format>
<quantity>collection</quantity>
<comment>
bowtie version 1.1.1 index of hs37d5_simple.fa and GRCm38mm10_simple.fa generated as follows:
bowtie-build -f hs37d5_simple.fa hs37d5_simple.fa
bowtie-build -f GRCm38mm10_simple.fa GRCm38mm10_simple.fa
</comment>
</filetype>
<filetype>
<identifier>miRBase_mature</identifier>
<format>fasta</format>
<quantity>single</quantity>
<comment>mature known miRNA reference from miRBase Release 20 uploaded to ASPERA</comment>
</filetype>
<filetype>
<identifier>miRBase_hairpin</identifier>
<format>fasta</format>
<quantity>single</quantity>
<comment>precursor (hairpin) known miRNA reference from miRBase Release 20 uploaded to ASPERA</comment>
</filetype>
</references>
<!-- Following section: list output files of process [e.g. bed files, wiggle tracks] -->
<outputs>
<filetype>
<identifier>SampleID.SXPv2.DATE.known.csv</identifier>
<format>csv</format>
<quantity>single</quantity>
<comment>
expression of known miRNAs quantified by miRDeep2
</comment>
</filetype>
<filetype>
<identifier>SampleID.SXPv2.DATE.known.bed</identifier>
<format>bed</format>
<quantity>single</quantity>
<comment>
BED track of expression of known miRNAs quantified by miRDeep2
</comment>
</filetype>
<filetype>
<identifier>SampleID.SXPv2.DATE.known.bedGraph</identifier>
<format>bedGraph</format>
<quantity>single</quantity>
<comment>
bedGraph track of expression of known miRNAs quantified by miRDeep2
</comment>
</filetype>
<filetype>
<identifier>SampleID.SXPv2.DATE.novel.bed</identifier>
<format>bed</format>
<quantity>single</quantity>
<comment>
bed track of expression of novel miRNAs predicted by miRDeep2
</comment>
</filetype>
<filetype>
<identifier>SampleID.SXPv2.DATE.novel.bedGraph</identifier>
<format>bedGraph</format>
<quantity>single</quantity>
<comment>
bedGraph track of expression of novel miRNAs predicted by miRDeep2
</comment>
</filetype>
</outputs>
<!-- Precise description of what this process does, what output is generated and what statistics are computed -->
<software>
<tool>
<name>generate_config</name>
<version>missing</version>
<command_line>
<![CDATA[
echo -ne "{SampleID.fastq}\tID1\n" > config
]]>
</command_line>
<loop>no looping</loop>
<comment>
this command creates the configuration file for miRDeep2 to use in order to locate the FASTQ library {SampleID.fastq} and assign
a 3-letter internal ID to it, in this case ID1
</comment>
</tool>
<tool>
<name>mapper.pl</name>
<version>miRDeep2.0.0.7</version>
<command_line>
<![CDATA[
mapper.pl config -d -e -h -j -k {Adaptor} -l 18 -m -p {genome_index} -s reads_collapsed.fa -t reads_vs_genome.arf -v -o 12 &> mapper_summary.log
]]>
</command_line>
<loop>no looping</loop>
<comment>
use the configuration file to locate the library; remove adaptor provided by {Adaptor};
collapse the reads to the file "read_collapsed.fa";
map to the reference and output the alignments in the file "reads_vs_genome.arf";
print out summary in "mapper_summary.log"
The ARF is a text-based format consisting of the following columns:
readID # the ID of the read
readLength # length of the read
start # start position of the alignment relative to the read
end # end position of the alignment relative to the read
readSeq # sequence of the read
chr # chromosome of reference where read maps
refLength # length of the reference sequence where read maps to
start # start position of reference sequence where read maps to
end # end position of reference sequence where read maps to
referenceSeq # reference sequence where read maps to
strand # strand of reference
mm # number of mismatches in the alignment
MAPQ-like-string # m==perfect match, M==mismatch
</comment>
</tool>
<tool>
<name>miRDeep2</name>
<version>miRDeep2.0.0.7</version>
<command_line>
<![CDATA[
miRDeep2.pl reads_collapsed.fa {genome} reads_vs_genome.arf {miRBase_mature} none {miRBase_hairpin} -t {Species} -P -d -v 2> miRDeep2.report.log
]]>
</command_line>
<loop>no looping</loop>
<comment>quantify known miRNAs and predict putative novel miRNAs across samples</comment>
</tool>
<tool>
<name>rename_according_to_metadata_standards</name>
<version>missing</version>
<command_line>
<![CDATA[
cp miRNAs_expressed_all_samples_DATE_t_TIME.csv {SampleID}.SXPv2.{DATE}.known.csv
]]>
</command_line>
<loop>no looping</loop>
<comment>rename output data file to conform to metadata naming standards</comment>
</tool>
<tool>
<name>mirdeep2_csv2bed.pl</name>
<version>missing</version>
<command_line>
<![CDATA[
mirdeep2_csv2bed.pl -r result_DATE_t_TIME.csv -p -T {SampleID}
cp known_pres_DATE_t_TIME_score-50_to_na.bed {SampleID}.SXPv2.{DATE}.known.bed
echo "track name=\"{SampleID}.novel_miRNAs\" description=\"novel miRNAs detected by miRDeep2 for {SampleID}\" visibility=2 itemRgb=\"On\"" > "{SampleID}.SXPv2.{DATE}.novel.bed"
cat "novel_pres_DATE_t_TIME_score-50_to_na.bed" >> "{SampleID}.SXPv2.{DATE}.novel.bed"
]]>
</command_line>
<loop>no looping</loop>
<comment>
Generate BED tracks from the total precursor read counts of known and novel miRNAs and rename them according to metadata standards.
This tool has been uploaded to ASPERA.
</comment>
</tool>
<tool>
<name>bed_to_bedGraph</name>
<version>missing</version>
<command_line>
<![CDATA[
gawk 'NR==3 {print "track type=bedGraph description=\"miRDeep2 known miRNAs\" visibility=2 color=0,0,255 altColor=255,0,0" > FILENAME"Graph"; print $1,$2,$3,$5 >> FILENAME"Graph"} NR>3 {print $1,$2,$3,$5 >> FILENAME"Graph"}' "{SampleID}.SXPv2.{DATE}.known.bed"
gawk 'NR==1 {print "track type=bedGraph description=\"miRDeep2 novel miRNAs\" visibility=2 color=0,0,255 altColor=255,0,0" > FILENAME"Graph"; print $1,$2,$3,$5 >> FILENAME"Graph"} NR>1 {print $1,$2,$3,$5 >> FILENAME"Graph"}' "{SampleID}.SXPv2.{DATE}.novel.bed"
]]>
</command_line>
<loop>no looping</loop>
<comment>convert BED tracks to bedGraph</comment>
</tool>
</software>
</process>