align
CIRCexplorer2 align
aligns fusion junction reads with TopHat2/TopHat-Fusion combined pipeline, followed by fetching non-colinear fusion junction reads.
Usage and option summary
Usage:
CIRCexplorer2 align [options] -G GTF (-g GENOME | -i INDEX1 -j INDEX2 | -i INDEX1 | -j INDEX1) -f FQ
Options:
-h --help Show help message.
-v --version Show version.
-G GTF --gtf=GTF Annotation GTF file.
-g GENOME --genome=GENOME Genome fasta file.
-i INDEX1 --bowtie1=INDEX1 Index files for Bowtie1 (used for TopHat-Fusion).
-j INDEX2 --bowtie2=INDEX2 Index files for Bowtie2 (used for TopHat2).
-p THREAD --thread=THREAD Running threads. [default: 10]
-f FQ --fastq=FQ Input file.
-o OUT --output=OUT Output directory. [default: alignment]
-b JUNC --bed=JUNC Output file. [default: back_spliced_junction.bed]
--bw Create BigWig file.
--scale Scale to HPB.
--skip-tophat Skip TopHat mapping.
--skip-tophat-fusion Skip TopHat-Fusion mapping.
Notes about options
- When offering reference genome, you could use genome sequence file (
-g GENOME
) or genome index files of bowtie1 and/or bowtie2 (-i INDEX1
and/or-j INDEX2
). - If you set
--bw
option, BigWig file of TopHat2 alignment would be created automatically for visualization. It will not consider strand information of read alignment. - If you set
--scale
option, expression levels (for BigWig file) would be scaled to HPB (Hits per billion-mapped-bases ). More information about HPB could be found in this paper. - If you set
--skip-tophat
, TopHat2 alignment would be skipped. It is useful for some specific conditions, please see FAQ for details. - If you set
--skip-tophat-fusion
, TopHat-Fusion alignment would be skipped. It is useful for poly(A)+ RNA-seq. - You could offer multiple fastq files (or compressed files) separated or comma.
- Only single-read RNA-seq is supported. It is recommended to convert paired-end RNA-seq to single-read RNA-seq before alignment.
- It will overwrite the output directory and output file automatically, so please be careful when setting the path of output directory.
- Because Tophat only supports Python2, you should ensure Python2 has been installed in your computer, even if you were running Python3 version of CIRCexplorer2.
Output
CIRCexplorer2 align
will create a folder(alignment
) and a file(back_spliced_junction.bed
). The back_spliced_junction.bed
would be used by other modules of CIRCexplorer2 to further annotate and characterize circular RNAs.
back_spliced_junction.bed
alignment
├── bowtie1_index/
├── bowtie2_index/
├── tophat/
├── tophat_fusion/
├── tophat.log
└── tophat_fusion.log
bowtie1_index
: Index file folder for Bowtie1.bowtie2_index
: Index file folder for Bowtie2.tophat
: TopHat2 alignment folder.tophat_fusion
: TopHat-Fusion alignment folder.back_spliced_junction.bed
: Fusion junction information file.tophat.log
: Log file of TopHat2 alignment.tophat_fusion.log
: Log file of TopHat-Fusion alignment.
Format of back_spliced_junction.bed
:
Field | Description |
---|---|
chrom | Chromosome |
start | Start of fusion junction |
end | End of fusion junction |
name | Fusion id/Junction reads |
score | No meaning |
strand | No meaning |