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bowtie2_seq
[bowtie2_seq] uses bowtie2 to map sequences in the stream against a specified index created with [create_bowtie2_index]. The resulting records are SAM type:
MAPQ: 42
STRAND: -
Q_ID: M01168:16:000000000-A1R9L:1:1101:16679:1790
S_ID: NODE_99_length_50022_cov_15.716165
REC_TYPE: SAM
TLEN: 498
S_BEG2: 32803
S_BEG: 32555
SEQ: TGGGAA (...)
CIGAR: 213M
Q_ID2: =
S_END: 32767
---
Bowtie2 must be installed for [bowtie2_seq] to work. Read more about bowtie2 here:
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
... | bowtie2_seq [options] <-i index>
[-? | --help] # Print full usage description.
[-i <string> | --index_name=<string>] # Choose target index (instead of genome).
[-t <string> | --type=<string>] # Library type <paired|single> - Default=single
[-m <uint> | --mismatches=<uint>] # Mismatches allowed (0-3) - Default=0
[-c <uint> | --cpus=<uint>] # Number of CPUs to use - Default=1
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
In order to use [bowtie2_seq] to map a stack of query sequences from a FASTA file to a specified genome previously formatted with [create_bowtie2_index], do:
read_fasta -i query_sequences.fna | bowtie2_seq -i Bowtie/hg19
To determine the distribution of template length from a paired-end library you need to make sure that the pairs are interleaved in the stream (use [order_pairs), and then do:
... | order_pairs | bowtie2_seq -i Bowtie/hg19 -t paired | plot_distribution -k TLEN -x
[create_bowtie2_index]
Martin Asser Hansen - Copyright (C) - All rights reserved.
January 2013
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
[bowtie2_seq] is part of the Biopieces framework.