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featureCounts - Online in the Cloud

Run featureCounts in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command featureCounts that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


featureCounts - a highly efficient and accurate read summarization program

USAGE


featureCounts [options] -a <annotation_file> -o <output_file> input_file1 [input_file2]
...

Required arguments:

-a <string>
Name of an annotation file. GTF format by default. See -F option for more formats.

-o <string>
Name of the output file including read counts. A separate file including summary
statistics of counting results is also included in the output (`<string>.summary')

input_files
List of input files in BAM or SAM format. Users do not need to specify it is BAM or
SAM.

Optional arguments:

-A <string>
Name of a comma delimited file including chromosome alias names used to match
chromosome names used in annotation with those used in BAM/SAM input, if they are
different. See Users Guide for file format.

-F <string>
Specify format of provided annotation file. Acceptable formats include `GTF' and
`SAF'. `GTF' by default. See Users Guide for description of SAF format.

-t <string>
Specify feature type in GTF annotation. `exon' by default. Features used for read
counting will be extracted from annotation using the provided value.

-g <string>
Specify attribute type in GTF annotation. `gene_id' by default. Meta-features used
for read counting will be extracted from annotation using the provided value.

-f Perform read counting at feature level (eg. counting reads for exons rather than
genes).

-O Assign reads to all their overlapping meta-features (or features if -f is
specified).

-s <int>
Perform strand-specific read counting. Possible values: 0 (unstranded), 1
(stranded) and 2 (reversely stranded). 0 by default.

-M Multi-mapping reads will also be counted. For a multimapping read, all its reported
alignments will be counted. The `NH' tag in BAM/SAM input is used to detect
multi-mapping reads.

-Q <int>
The minimum mapping quality score a read must satisfy in order to be counted. For
paired-end reads, at least one end should satisfy this criteria. 0 by default.

-T <int>
Number of the threads. 1 by default.

-v Output version of the program.

-J Count number of reads supporting each exon-exon junction. Junctions were
identified from those exon-spanning reads in the input (containing 'N' in CIGAR
string). Counting results are saved to a file named '<output_file>.jcounts'

-G <string>
The Fasta file containing the reference genome used in generating the input SAM or
BAM files. This argument is only needed when doing junction counting.

-R Output detailed assignment result for each read. A text file will be generated for
each input file, including names of reads and meta-features/features reads were
assigned to. See Users Guide for more details.

--largestOverlap
Assign reads to a meta-feature/feature that has the largest number of overlapping
bases.

--minOverlap <int>
Specify minimum number of overlapping bases required between a read and a
meta-feature/feature that the read is assigned to. 1 by default.

--read2pos <5:3>
Reduce reads to their 5' most base or 3' most base. Read counting is then performed
based on the single base the read is reduced to.

--readExtension5 <int> Reads are extended upstream by <int> bases from their
5' end.

--readExtension3 <int> Reads are extended upstream by <int> bases from their
3' end.

--fraction
Use a fractional count 1/n, instead of 1 (one) count, for each reported alignment
of a multi-mapping read in read counting. n is total number of alignments reported
for the multi-mapping read. This option must be used together with '-M' option.

--primary
Count primary alignments only. Primary alignments are identified using bit 0x100 in
SAM/BAM FLAG field.

--ignoreDup
Ignore duplicate reads in read counting. Duplicate reads are identified using bit
Ox400 in BAM/SAM FLAG field. The whole read pair is ignored if one of the reads is
a duplicate read for paired end data.

--countSplitAlignmentsOnly Count split alignments only (ie. alignments with
CIGAR string containing `N'). An example of split alignments is exon-spanning reads
in RNA-seq data.

-p Count fragments (read pairs) instead of individual reads. For each read pair, its
two reads must be adjacent to each other in BAM/SAM input.

-P Check validity of paired-end distance when counting read pairs. Use -d and -D to
set thresholds.

-d <int>
Minimum fragment/template length, 50 by default.

-D <int>
Maximum fragment/template length, 600 by default.

-B Count read pairs that have both ends successfully aligned only.

-S <ff:fr:rf>
Specify orientation of two reads from the same pair, 'fr' by by default
(forward/reverse).

-C Do not count read pairs that have their two ends mapping to different chromosomes
or mapping to same chromosome but on different strands.

--donotsort
Do not sort reads in BAM/SAM input. Note that reads from the same pair are required
to be located next to each other in the input.

--maxMOp <int>
Maximum number of 'M' operations allowed in a CIGAR string . 10 by default. Both
'X' and '=' are treated as 'M' and adjacent 'M' operations are merged in the CIGAR
string.

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