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Posted by / 29-Aug-2017 19:13

Bwa single end

When multiple lanes of data are combined # from separate BAM files, read groups provide identification of the # source of each read.Variant callers such as GATK depend on # having well-defined read group information.

In this hands-on will learn how to align DNA and RNA-seq data with most widely used software today.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: $RG"; echo "---------------------------------------------------------"; # ------------------ # Error Checks # ------------------ # Make sure the fastq file(s) exist.needed because # programs don't always return non-0 return # codes, and worse, they also create their # output file with 0 length so that just # checking for its existence is not enough # to ensure the program ran properly ck File Sz() # -------------- # Defaulting # -------------- # If aligning read pairs, find the name of the R2 file # based on the R1 filename.if [ "$PAIRED" == "1" ]; then IN_FQ_R1="$IN_FQ"; IN_FQ_R2=$; fi # Find the path of the BWA reference based on the assembly # name provided.

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You can download it from Dropbox data or from the , you get it in only one step by going to: Ensembl GRCh37 GRCh38 should see a species table with a Human ( quality 1% mutations.

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