Results for "BAM"

Bio-Scripts

  • Genome Covered !

    zero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4==0 {bpCountZero+=($3-$2)} {print bpCountZero}' | tail -1) nonzero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4>0 {bpCountNonZero+=($3-$2)} {print bpCountNonZero}' | tail -1) percent=$(bc

    2172 days ago

  • Coverage / Depth of reads !

    # get total number of bases covered at MIN_COVERAGE_DEPTH or higher samtools mpileup mapping_result_sorted.bam | awk -v X="${MIN_COVERAGE_DEPTH}" '$4>=X' | wc -l 32876 # get le...

    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.bai

    2146 days ago

  • Running Trinity on RNA-seq !

    ...yrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" * Running CMD: /home/urbe/...yrnaseq-Trinity-v2.6.6/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /home/urbe/Tools/trinityrnase...

    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

  • Running REAPR !

    ...ed.iteration1.fa out.smaltmap.bam out.pipeline" cd out.pipel...00.assembly.fa.gaps.gz 00.in.bam 01.stats $fcdcutoff 03.score...ed.iteration1.fa out.smaltmap.bam out.pipeline cd out.pipeline...ed.iteration1.fa out.smaltmap.bam out.pipeline perfect echo "...

    2062 days ago

  • Installing NextSV on Ubuntu !

    ...6%] Built target zlibstatic Scanning dependencies of target BamTools-static [ 17%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles...%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/T...

    2061 days ago

  • Downloading GATK !

    ...encing data into an unmapped SAM or BAM file. MarkIlluminaAdapte...card) Reads a SAM or BAM file and rewrites it with new...ects quality yield metrics from SAM/BAM/CRAM file(s). CollectRaw...Outputs reads from a SAM/BAM/CRAM by read group, sample an...

    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 treatBAMfile

    2018 days ago