Alignment - mlbendall/telescope_tutorial GitHub Wiki
module load bowtie2
bowtie2 --help
Output should look like this:
Bowtie 2 version 2.2.9 by Ben Langmead ([email protected], www.cs.jhu.edu/~langmea)
Usage:
bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]
<bt2-idx> Index filename prefix (minus trailing .X.bt2).
NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
<m1> Files with #1 mates, paired with files in <m2>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<m2> Files with #2 mates, paired with files in <m1>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<r> Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<sam> File for SAM output (default: stdout)
<m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.
Inputs for bowtie2
include the reference genome and the paired-end fastq files.
Important arguments for Telescope:
--very-sensitive-local
Find local alignments with high sensitivity
--score-min L,0,1.6
Report alignments that are approximately 95% similar
-k 100
Report up to 100 alignments
The reference genome we are using, hg19, is located at /lustre/groups/nixonlab/References/hg19
.
The index is found at /lustre/groups/nixonlab/References/hg19/Sequence/Bowtie2Index/genome
ref=/lustre/groups/nixonlab/References/hg19/Sequence/Bowtie2Index/genome
bowtie2 \
--very-sensitive-local -k 100 --score-min L,0,1.6 \
-x $ref \
-1 SRR1686362/SRR1686362_pass_1.fastq.gz \
-2 SRR1686362/SRR1686362_pass_1.fastq.gz \
-S SRR1686362/aligned.sam
We can examine the output using samtools
:
module load samtools/1.3.1
samtools view SRR1686362/aligned.sam
Finally, with this alignment we can run Telescope
module load telescope/0.3.1
telescope id \
--outdir SRR1686362 \
--exp_tag inform \
--verbose \
--out_matrix \
--updated_sam \
--thetaPrior 100000 \
SRR1686362/aligned.sam