Bwa single end Chattanooga naked

Posted by / 26-Jun-2017 08:45

Bwa single end

Do this before running # checks so user can see what went wrong.echo "================================================================="; echo "align_- `date`"; if [ "$PAIRED" == "1" ]; then echo " fastq read1 file: $IN_FQ_R1"; echo " fastq read2 file: $IN_FQ_R2"; else echo " input file: $IN_FQ"; fi echo " output prefix: $OUT_PFX"; echo " assembly: $ASSEMBLY"; echo " bwa version: $BWA_VER"; echo " ref prefix: $REF_PFX"; echo " read group line: $RG"; echo "---------------------------------------------------------"; # ------------------ # Error Checks # ------------------ # Make sure the fastq file(s) exist.# Here we set the RG variable to be the read group line we want # inserted in the header.READ_GRP=$OUT_PFX; RG='@RG\t ID:1\t PL: ILLUMINA\t SM:'$READ_GRP'\t DS:ref='$ASSEMBLY',pfx='$REF_PFX # Display how the program will be run, including # defaulted arguments.Two different datasets, high and low quality have been simulated for DNA, high quality contains 0.1% of mutations and low quality contains 1%.For RNA-seq a 100bp and 150bp datasets have been simulated.

"bwa aln"; ck File Sz "$OUT_PFX.sai"; echo "---------------------------------------------------------"; echo "Running bwa samse"; echo "---------------------------------------------------------"; bwa samse -r "$RG" $REF_PFX $OUT_$IN_FQ | samtools view -b -S - $OUT_PFX.bam; ck Res $?: $ # Note: reference indexes created with bwa 0.5.9 are *not* # compatible with bwa 0.6 or higher.So we go to some # trouble to figure out which BWA version we have BWA_VER=`bwa 2&1 | grep Version | awk '' | awk -F '.' ''`; if [ "$BWA_VER" == "0.5" ]; then BWA_DIR=bwa; elif [ "$BWA_VER" == "0.6" ]; then BWA_DIR=bwa6; else BWA_DIR=unknown_bwa_version; fi REFBASE="$WORK_COMMON/ref_genome/$BWA_DIR/base" if [ "$ASSEMBLY" == "hg18" ]; then REF_PFX="$REFBASE/ucsc/$ASSEMBLY/Homo_sapiens_assembly18.fasta"; elif [ "$ASSEMBLY" == "hg19" ]; then REF_PFX="$REFBASE/ucsc/$ASSEMBLY/ucsc.hg19.fasta"; elif [ "$ASSEMBLY" == "ecoli" ]; then REF_PFX="$REFBASE/misc/$ASSEMBLY/REL606.5.fasta"; else REF_PFX="$REFBASE/ucsc/$ASSEMBLY/$.fa"; fi # Read group information is part of the SAM/BAM header that desribes # what is being aligned.Building a whole genome index requires a lot of RAM memory and almost one hour in a typical workstation, for this reason in this tutorial we will work with chromosome 21 to speed up the exercises.The same steps would be done for a whole genome alignment.

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