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FileNaming_History.txt
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########## CHIP-SEQ PIPELINE VERSION 4 ###########
All outputs will get a version name identifier:
B3 means that the single-end Sam file was created with this pipeline version
B4 means that paired-end Sam file was created with this pipeline version
W4 means that the peak/bedgraph/wiggle files were made with this pipeline version
B3W3 means that the everything was made with this pipeline version
All output files will also may also get the following identifiers within their names:
PE will indicate Bowtie and/or MACS2 will treat the files as paired-end reads.
The mapped read length will be listed as Xbp where X is the number of bases aligned when the length is not 50bp.
SAM:
All new sam files will be given the following names: $TAG-$GENROOT.sam
where $TAG is the user defined name and $GENROOT is one of the following:
- SK1Yue-PM
- SK1Yue-2mis
- SacCer3-2mis
- SK1K-PM
- SacCer3-rDNA
- SK1K-rDNA
MACS2 FOLDER:
Macs2 files will now go in folders with the notation: $TAGC-$GEN-$VER-MACS2 where
$TAGC is either the tagname of the ChIP file or the user-defined name $REP,
$GEN is either SacCer3 or SK1K, and
$VER will currently be either B3W4/B4W4, 2mis_W4, or PM_W4.
$FLMKR will be incorporated into all MACS2 output files.
The term "Reps" will be incorporated into all MACS2 output files when applicable.
MACS2 FILES:
See MACS2 FOLDER with the following changes:
All files will include the method of Bowtie analysis: 2mis, PM, or rDNA.
Wiggle and bedgraph files will include the normalization method: FE.
ChIP vs ChIP analysis is identified as ChvCh.
########## CHIP-SEQ PIPELINE VERSION 3 ###########
All outputs will get a version name identifier:
B3 means that the Sam file was created with this pipeline version
W3 means that the peak/bedgraph/wiggle files were made with this pipeline version
B3W3 means that the everything was made with this pipeline version
SAM:
All new sam files will be given the following names: $TAG-$GENROOT.sam where $TAG is the user defined name and $GENROOT is one of the following:
SK1Yue-PM_B3
SK1Yue-2mis_B3
SacCer3-2mis_B3
SK1K-PM_B3
SacCer3-rDNA_B3
SK1K-rDNA_B3
MACS2 FOLDER:
Macs2 files will now go in folders with the notation: $TAGC-$GEN-$VER-MACS2 where
$TAGC is either the tagname of the ChIP file or the user-defined name $REP,
$GEN is either SacCer3 or SK1K, and
$VER will currently be either B3W3, 2mis_W3, or PM_W3.
$FLMKR will be incorporated into all MACS2 output files.
The term "Reps" will be incorporated into all MACS2 output files when applicable.
MACS2 FILES:
See MACS2 FOLDER with the following changes:
All files will include the method of Bowtie analysis: 2mis, PM, or rDNA.
Wiggle and bedgraph files will include the normalization method: FE.
ChIP vs ChIP analysis is identified as either: ChvCh or InvIn.
########## CHIP-SEQ PIPELINE VERSION 2 ###########
SAM:
All new sam files will be given the following names: $TAG-$GENROOT.sam where $TAG is the user defined name and $GENROOT is one of the following:
SK1K-PM
SacCer3-2mis
MACS2 FOLDER:
Macs2 files will now go in folders with the notation: $TAGC-MACS2 where
$TAGC is either the tagname of the ChIP file or the user-defined name $REP
MACS2 FILES:
Macs2 files will be named with the following base: $TAGC-$GENROOT-M$MLOW_MACS2 where
$TAGC is either the tagname of the ChIP file or the user-defined name $REP,
and $MLOW is listed only when model-building is enabled.
Replicates:
When replicates are combined, a new BAM file is created called $REP-$FLMKR-reps-$GENROOT.bam for the ChIP file
and $REP-$FLMKR_input-reps-$GENROOT.bam for the input file.
Also "rep" and the filemaker IDs were incorporated into every file and folder created as part of the MACS2 analysis.
Double-normalization was also possible for wiggle-files only.
########## CHIP-SEQ PIPELINE VERSION 1 ###########