2172 days ago
2172 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
BAM files and mapping BESST requires sorted and indexed BAM files as input. Any read aligner + samtools can be used to obtain...ter/scripts/reads_to_ctg_map.py) for obtaining sorted and indexed BAM files with BWA-mem or BWA-sam...2087 days ago
Bash script to convert SAM to BAM visualization ready
samtools view -bS file.sam | samtools sort - file_sorted samtools index test_sorted.bam test_sorted.bai2146 days ago
2090 days ago
Long reads mapper bash script !
...les ready for visualization !" $samtools view -Sb $fileName.out.sam | $samtools sort -m 4G -@$thread -o $fileName.sorted.bam - && $samtools index -@$thread $fileName.sorted.bam echo "All Done :)"2085 days ago
2062 days ago
2061 days ago
2038 days ago
Generates a genome coverage plot with R
library(CoverageView) ##draw a coverage plot for a test case BAM file #get a BAM test file treatBAMfile2018 days ago