search

CAFS-bioinformatics / P_RNA_scaffolder

use paired-end transcriptome reads to scaffold genomes
10 stars 3 forks source link

working with bam instead of sam #3

Open michieitel opened 4 years ago

michieitel commented 4 years ago

Hi!

I am wondering how to work with bam files instead of sam? I have sam files that are >300Gb for multiple assemblies due to the high amount of short read data I have.

I tried using bam files calling this command:

for file in *fasta;do 
   mkdir ${file%.fasta}_scaffolded; 
   /home/meitel/tools/P_RNA_scaffolder/P_RNA_scaffolder.sh -o ${file%.fasta}_scaffolded -d /home/meitel/tools/P_RNA_scaffolder -i $( samtools view -h ${file%.fasta}.bam ) \
   -j $file -F $R1 -R $R2 -b yes -p 0.95 -t $NUMTH -f 10 -n 1000 ; 
   echo "done"
done

but it threw a memory allocation error complaining that 18million Gb (!) or ram could not be allocated.

Any ideas on how to use bams?

Thanks Michael