Hi Dengfeng,
I am trying to evaluate a 10X Chromium assembly done with SUPERNOVA.
I can get the gap.bed file, but the following never finished:
#####################################################
bwa index Andean12nov19_SUPERNOVA_output_pseudohap2.1.fasta
while read -r r1 r2
do
prefix=basename $r1 .fastq.gz
/home/sgod/GenomicsPrograms/asset/bin/10x -c -p $prefix $r1 $r2 # generate trimmed read files $prefix_{1,2}.fq.gz
bwa mem -t12 Andean12nov19_SUPERNOVA_output_pseudohap2.1.fasta $prefix_1.fq.gz $prefix_2.fq.gz | samtools view -b - > $prefix.bam
done < $10xlist
/home/sgod/GenomicsPrograms/asset/bin/ast_10x gaps.bed $bam1 $bam2 $bam3 ... >10x.bed 2>ast_10x.log
#####################################################
My 10Xlist is a file with the directory and 4 fastq files from the original 10X sequencing (R1 and R2 X 2 lanes)
Is there something simple I am missing in the syntax?
Thank you for your input!
Sher
Hi Dengfeng,
I am trying to evaluate a 10X Chromium assembly done with SUPERNOVA.
I can get the gap.bed file, but the following never finished:
#####################################################
bwa index Andean12nov19_SUPERNOVA_output_pseudohap2.1.fasta
while read -r r1 r2
do
prefix=
basename $r1 .fastq.gz/home/sgod/GenomicsPrograms/asset/bin/10x -c -p $prefix $r1 $r2 # generate trimmed read files $prefix_{1,2}.fq.gz
bwa mem -t12 Andean12nov19_SUPERNOVA_output_pseudohap2.1.fasta $prefix_1.fq.gz $prefix_2.fq.gz | samtools view -b - > $prefix.bam
done < $10xlist
/home/sgod/GenomicsPrograms/asset/bin/ast_10x gaps.bed $bam1 $bam2 $bam3 ... >10x.bed 2>ast_10x.log
#####################################################
My 10Xlist is a file with the directory and 4 fastq files from the original 10X sequencing (R1 and R2 X 2 lanes)
Is there something simple I am missing in the syntax?
Thank you for your input!
Sher