Results for "Merge"
Bio-Scripts
Perl script to merge LastZ overlaps
#!/usr/bin/perl use strict; use warnings; use 5.010; # Filter out the exact/direct overlaps from tab seperated alignment file. (lastz format=general- ready) # Do not inclide header in lastz outfile # USAGE: perl filterOverlaps.pl infile > outfile open my $fh, '2115 days ago
- ...or transcriptome file in FASTA format --threads= Number of threads to use (default: 8) --merge-assemblies= Merge best contigs from multiple as...
2113 days ago
- ...tes on Spark MarkDuplicatesWithMateCigar (Picard) Identifies duplicate reads, accounting for mate CIGAR. MergeBamAlignment (Picard) Merge alignment data from a SAM or...
2065 days ago
- (denovo_asm) [jnarayan@hmem00 ~]$ git clone https://github.com/cdunn2001/git-sym.git fatal: destination path 'git-sym' already exists and is not an empty directory....
2024 days ago
To convert just one specific read group to fastq
...qToSam F1=reads/{}_1.fastq F2=reads/{}_1.fastq O=bam/{}.bam RG=GROUP-{} LB=LIB-{} SM=SAMPLE_{} QUIET=true 2>> log.txt" # Merge all the BAM files into one. samtools merge -f all.bam bam/*.bam # Inv...1532 days ago
Bash script to get exon fragments from genome files !
#Exons are already defined in the GTF file, so we simply need to print lines that are marked exonic. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="exon" {print $1,$4-1,$5}' | bedtools sort | bedtools merge -i - | gzip > my_exon.bed.gz1355 days ago
Bash script to handle Multifasta files
...tput.fasta #Match FASTA headers in two different multi-FASTA files $ awk 'NR=FNR{a[$0];next}$0 in a{print $0}' input1.fasta input2.fasta #Merge all FASTA files in a director...1347 days ago
- ...-devtools intltool jq libalgorithm-merge-perl libarchive-cpio-perl lib...-devtools intltool jq libalgorithm-merge-perl libarchive-cpio-perl lib...ntu bionic/main amd64 libalgorithm-merge-perl all 0.08-3 [12.0 kB]...ly unselected package libalgorithm-merge-perl. Preparing to unpack .....
1044 days ago
Corona variant calling steps !
...results/bcf/*.vcf.gz Variant_Results_of_COVID_gz/ rem cp -r results/bcf/*.vcf.gz.tbi Variant_Results_of_COVID_gz/ bcftools merge results/bcf/*.vcf.gz -Oz -o Merge_Final_Variants.vcf.gz gunzip...1035 days ago
Tadpole is 250x faster than SPADes assembler !
...ne like this: tadpole.sh in=libA_r1.fq,libA_merged.fq in2=libA_r2.fq,null extra=libB_r1.fq out=ecc_libA_r1.fq,ecc_libA_merged.fq out2=ecc_libA_r2.fq,null...ters (for overlapping paired-end reads only): merge=f Attempt to merg...966 days ago
