Good morning, everyone,
I am trying to apply a damage pattern using gargammel.pl to a sample trying to generate an output with 5X coverage. The command line used for gargammel was:
gargammel.pl -n -comp 0,0,1 -l -ss HS25 -damage v,l,d,s -o /sample_gargammel_output/ /input
The -n flag specified the number of reads corresponding to a sample with 5X coverage. a bug was noticed in ART during programme execution, as it showed an automatic setting of the flag -c 1. Therefore the _a.fa output of gargammel was used to re-run ART by manually setting the -f 5 parameter. The fastqc of the outputs _s1.fq and _f2.fq were found to be good. then AdapterRemoval was run with the following command:
AdapterRemoval --file1 _s1.fq --file2 _s2.fq --minlength 30 --minquality 25 --trimns --trimqualities --basename file_collapsed.fq --collapse
a FastQC was then performed and then alignment was performed to obtain the BAM.
bwa mem /reference.fasta paired.collapsed > paired.collapsed.sam
samtools view -Sb paired.collapsed.sam > paired.collapsed.bam
samtools sort paired.collapsed.bam > paired.sorted.bam
dedup -i paired.sorted.bam -m -o /directory_dedup
The QualiMap, however, showed coverage between 0 and 1X. Has this happened to anyone yet? Do you know how to solve the problem and maintain a coverage of 5X in my resulting BAM?
