diff --git a/Cuernavaca/slides/Cuernavaca.md b/Cuernavaca/slides/Cuernavaca.md index 44def83..1145a95 100644 --- a/Cuernavaca/slides/Cuernavaca.md +++ b/Cuernavaca/slides/Cuernavaca.md @@ -366,6 +366,11 @@ bowtie2 -x data/zika -1 data/Zika-envelope.n1E4.R1.fastq.gz \ +* Workflow +![Schematic of bioinformatic workflow for adaptive reference mapping](workflow.png) + + + # ¿Funciona? * Try remapping FASTQ files to new reference @@ -486,6 +491,29 @@ sandbox/slice-1700-2000.nwk * Need to be cautious about mapping to similar references because adaptive algorithm can cause collisions +* Try using `bowtie2` and `adapt-ref.py` on the following files: + * `mixed-references.fa` + * `mixed.R1.fastq` + * `mixed.R2.fastq` + + + +# My workflow: +``` + 606 bowtie2-build -q -f data/mixed-references.fa sandbox/mixed-ref + 607 bowtie2 -x sandbox/mixed-ref -1 data/mixed.R1.fastq.gz -2 data/mixed.R2.fastq.gz -S sandbox/mixed.sam --local + 608 python scripts/adapt-ref.py -h + 609 python scripts/adapt-ref.py sandbox/mixed.sam data/mixed-references.fa sandbox/mixed.fa + 610 bowtie2-build -q -f sandbox/mixed.fa sandbox/mixed-ref1 + 611 bowtie2 -x sandbox/mixed-ref1 -1 data/mixed.R1.fastq.gz -2 data/mixed.R2.fastq.gz -S sandbox/mixed2.sam --local + 612 python scripts/adapt-ref.py sandbox/mixed2.sam sandbox/mixed.fa sandbox/mixed2.fa + 613 bowtie2-build -q -f sandbox/mixed2.fa sandbox/mixed-ref2 + 614 bowtie2 -x sandbox/mixed-ref2 -1 data/mixed.R1.fastq.gz -2 data/mixed.R2.fastq.gz -S sandbox/mixed3.sam --local +``` + + +# Have a look at your work in Tablet! + # Advertencias diff --git a/Cuernavaca/slides/images/workflow.png b/Cuernavaca/slides/images/workflow.png new file mode 100644 index 0000000..9e03bde Binary files /dev/null and b/Cuernavaca/slides/images/workflow.png differ