diff --git a/README-alt.md b/README-alt.md index f4d3a45..d46b38f 100644 --- a/README-alt.md +++ b/README-alt.md @@ -14,13 +14,13 @@ wget ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/H gzip -d GCA_000001405.15_GRCh38_full_analysis_set.fna.gz mv GCA_000001405.15_GRCh38_full_analysis_set.fna hs38a.fa bwa index hs38a.fa -cp bwa-hs38-res/hs38d4.fa.alt hs38a.fa.alt +cp bwa-hs38-bundle/hs38d4.fa.alt hs38a.fa.alt ``` Perform mapping: ```sh bwa mem hs38a.fa read1.fq read2.fq \ - | bwa-hs38-res/k8-linux bwa-postalt.js hs38a.fa.alt \ + | bwa-hs38-bundle/k8-linux bwa-postalt.js hs38a.fa.alt \ | samtools view -bS - > aln.unsrt.bam ``` For short reads, the postprocessing script `bwa-postalt.js` runs at about the @@ -30,14 +30,14 @@ same speed as BAM compression. Construct the index: ```sh -cat hs38a.fa bwa-hs38-res/hs38d4-extra.fa > hs38d4.fa +cat hs38a.fa bwa-hs38-bundle/hs38d4-extra.fa > hs38d4.fa bwa index hs38d4.fa -cp bwa-hs38-res/hs38d4.fa.alt . +cp bwa-hs38-bundle/hs38d4.fa.alt . ``` Perform mapping: ```sh bwa mem hs38d4.fa read1.fq read2.fq \ - | bwa-hs38-res/k8-linux bwa-postalt.js -p postinfo hs38d4.fa.alt \ + | bwa-hs38-bundle/k8-linux bwa-postalt.js -p postinfo hs38d4.fa.alt \ | samtools view -bS - > aln.unsrt.bam ``` This command line generates `postinfo.ctw` which loosely evaluates the presence