I am trying to run a PE library through bowtie2 and then into svDetect for Circos.
Bowtie2 run with
module load Bowtie2/2.3.4.1-foss-2016b
bowtie2 -x w82 -1 SRR2163311_1.fastq.gz -2 SRR2163311_2.fastq.gz --un-conc unPEK.sam --al-conc alPEK.sam --met-file metPEK.txt -S samPEK.sam
My output provides me with alPEK.1.sam, alPEK.2.sam, samPEK.sam as well as in .txt.
Trying svDETECT with .conf file as (have tried using a comma to list both on the alPEK.sams)
general
input_format = sam
sv_type = all
mates_orientation=FR
read1_length=90
read2_length=90
mates_file=alPEK.sam
cmap_file=gm20.len
output_dir=results
tmp_dir=tmp
num_threads=14
general
detection
split_mate_file=1
window_size=750 step_length=150
/detection
filtering
split_link_file=0
strand_filtering=1
Output with error
# Linking procedure ...
-- file=/scratch/sxd/workDir/svDETbase/alPEK.sam
-- input format=sam
-- type=all
-- read1length=90, read2length=90
-- window size=750, step length=150 /usr/local/apps/eb/SVDetect/0.7-foss-2016b-Perl-5.24.1/bin/SVDetect:
can't open /scratch/sxd/workDir/svDETbase/alPEK.sam:No such file or
directory
Is it possible to input both .1.sam & .2.sam? I did try view/merge via samtools but unsuccessful. Is the bowtie2 output salvageable for svDetect or should I start over with BWA?
thanks!
Thank you! I will opt for bwa mem then. I also appreciate the newer alternatives. I will get this running but thank you very much!
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