Results for "View"
Bio-Scripts
Needleman-Wunsch Algorithm in Perl
#!/usr/bin/perl # USAGE: perl nw.pl HEAGAWGHEE PAWHEAE BLOSUM50.txt -8 # See: "Biological sequence anaysis" Durbin et al. ed. CUP 1998, Pg. 19 # Needleman...2890 days ago
Install ATOM editor on Elemantory OS / Ubuntu
...build, rebuild-module-cache, remove, rm, search, show, star, starred, stars, test, uninstall, unlink, unpublish, unstar, update, upgrade, view. Run `apm help ` to see th...1161 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.bai2168 days ago
- ...ty-v2.6.6/trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100 /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/both.fa | samtools view -@ 40 -F4 -Sb - | samtools so...
2112 days ago
Long reads mapper bash script !
...thread -o $fileName.out.sam else echo "Unknown mapper name and parameter !" fi echo "Getting files ready for visualization !" $samtools view -Sb $fileName.out.sam | $samt...2108 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 $...1989 days ago
- bwa aln -t 8 targetGenome.fa reads.fastq | bwa samse targetGenome.fa - reads.fastq\ | samtools view -bt targetGenome.fa - | samtools sort - reads.bwa.targetGenome samtools index reads.bwa.targetGenome.bam
1819 days ago
Samtools commands for bioinformatician !
...: output file name samtools view -b -S -o sal_sej.bam sal_sej.sam ### viewing bam files (view command)...potential variants bcftools view -c -v sal_vars.bcf > sal_vars...nvert BAM to FASTA: samtools view filename.bam | awk '{OFS="\t"...1588 days ago
Bash script to alignment of short reads against reference genome !
...astq.gz SRR1770413_2.fastq.gz \ | samtools view -b - >SRR1770413.raw.bam sam...the second mate. #conversion to BAM: samtools view -b - --- this reads SAM from...astq.gz SRR341549_2.fastq.gz \ | samtools view -b - >SRR341549.raw.minimap2....1544 days ago
To convert just one specific read group to fastq
...he readgroups in the header. echo "" echo "SAM file header:" samtools view -H all.bam echo "" echo "Number of alignments with read group: GROUP-SRR1972919" samtools view -c -r GROUP-SRR1972919 all.ba...1527 days ago
