| genePredToGtf |
genePredToGtf database genePredTable output.gtf |
Convert genePred table or file to gtf. |
| GffCompare |
gffcompare [options]* {-i <input_gtf_list> | <input1.gtf> [<input2.gtf> .. <inputN.gtf>]} |
Compare, merge, annotate and estimate accuracy of one or more GFF files (the “query” files), when compared with a reference annotation (also provided as GFF). |
| GEMINI annotate |
gemini load -v my.vcf -t snpEff my.db |
It is inevitable that researchers will want to enhance the GEMINI framework with their own, custom annotations. GEMINI provides a sub-command called annotate for exactly this purpose. |
| StringTie |
stringtie <aligned_reads.bam> [options]* |
This is a special usage mode of StringTie, distinct from the assembly usage mode. In the merge mode, StringTie takes as input a list of GTF/GFF files and merges/assembles these transcripts into a non-redundant set of transcripts. This mode is used in the new differential analysis pipeline to generate a global, unified set of transcripts (isoforms) across multiple RNA-Seq samples. If a reference annotation is provided, StringTie will assemble the transfrags from the input GTF files with the reference transcripts. |
| AnnotateTable.py |
AnnotateTable.py -i mytable -a rmsk.gtf.gz -u -c1,2,3 -n rmsk -o mytable_rmsk |
AnnotateTable.py annotates individual positions of a table file according to annotations indexed by tabix tool. It adds from 1 to 3 additional columns according to -c option. |
| GeneTrack |
genetrack.py [options] input_paths |
GeneTrack separately identifies peaks on the forward "+†(W) and reverse “-†(C) strand. |
| pints_caller |
pints_caller --file-prefix FILE_PREFIX --bw-pl [BW_PL ...] --bw-mn [BW_MN ...] |
Identify transcriptional regulatory elements (enhancers and promoters) from sequencing libraries of transcription start site assays |
| pints_caller |
pints_caller --file-prefix FILE_PREFIX --bam-file [BAM_FILE ...] [--exp-type GROcap,etc.] |
Identify transcriptional regulatory elements (enhancers and promoters) from sequencing libraries of transcription start site assays
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