2028 days ago
2013 days ago
1997 days ago
CollectGcBiasMetrics.jar will generate a GC bias plot for each contig
samtools index aln-pe.mapped.sorted.bam for i in $(samtools view -H aln-pe.mapped.sorted.bam | awk -F"\t" '/@SQ/{gsub("^SN:","",$2);print $2}' ); do samtools view -b aln-pe.mapped.sorted.bam $i > aln-pe.mapped.sorted.$i....1997 days ago
1827 days ago
1598 days ago
Samtools commands for bioinformatician !
...amtools view -b -S -o sal_sej.bam sal_sej.sam ### viewing ba...atches samtools -F 4 sal_sej.bam | less ### count reads (..._ref_sej.fasta sal_sej_sorted.bam.bam > sal_vars.bcf ### c...ls depth -a sorted_dupremoved.bam | awk '{c++; if($3>0) total+=...1596 days ago
Bash script to alignment of short reads against reference genome !
...gz \ | samtools view -b - >SRR1770413.raw.bam sambamba sort SRR1770413.raw.bam sa...e second file the second mate. #conversion to BAM: samtools view -b - --- this...| samtools view -b - >SRR341549.raw.minimap2.bam sambamba sort SRR341549.raw....1553 days ago
To convert just one specific read group to fastq
...-dump -O reads -X 1000 --split-files {} # Create a directory for bam files mkdir -p bam # Generate a separate BAM...roups to paired files. samtools fastq -t -1 all1.fq -2 all2.fq all.bam # To convert just one spec...1536 days ago
picard tools command to get some insert statistics
#picard tools to get some insert statistics to see whether our reads seem to be in the correct place #module load picard/2.0.1 java -Xmx16g -XX:PermSize=8g -jar $...1330 days ago