From ff095c8047abd6e0ed741e5be3d55e2a040e7359 Mon Sep 17 00:00:00 2001 From: Hasindu Gamaarachchi Date: Wed, 20 Dec 2023 15:05:47 +1100 Subject: [PATCH] Update example-usage.md --- _docs/example-usage.md | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/_docs/example-usage.md b/_docs/example-usage.md index 9d840019..2aaa1a84 100644 --- a/_docs/example-usage.md +++ b/_docs/example-usage.md @@ -10,24 +10,26 @@ Follow the same steps as in [Nanopolish tutorial](https://nanopolish.readthedocs wget -O f5c_na12878_test.tgz "https://f5c.page.link/f5c_na12878_test" tar xf f5c_na12878_test.tgz -###### Using FAST5 as input ###### +###### Using S/BLOW5 as input (recommended) ###### #index, call methylation and get methylation frequencies -f5c index -d chr22_meth_example/fast5_files chr22_meth_example/reads.fastq -f5c call-methylation -b chr22_meth_example/reads.sorted.bam -g chr22_meth_example/humangenome.fa -r chr22_meth_example/reads.fastq > chr22_meth_example/result.tsv - +f5c index --slow5 chr22_meth_example/reads.blow5 chr22_meth_example/reads.fastq +f5c call-methylation --slow5 chr22_meth_example/reads.blow5 -b chr22_meth_example/reads.sorted.bam -g chr22_meth_example/humangenome.fa -r chr22_meth_example/reads.fastq > chr22_meth_example/result.tsv +f5c meth-freq -i chr22_meth_example/result.tsv > chr22_meth_example/freq.tsv #event alignment -f5c eventalign -b chr22_meth_example/reads.sorted.bam -g chr22_meth_example/humangenome.fa -r chr22_meth_example/reads.fastq > chr22_meth_example/events.tsv +f5c eventalign --slow5 chr22_meth_example/reads.blow5 -b chr22_meth_example/reads.sorted.bam -g chr22_meth_example/humangenome.fa -r chr22_meth_example/reads.fastq > chr22_meth_example/events.tsv -###### Using SLOW5 as input ###### + +###### Using FAST5 as input ###### #index, call methylation and get methylation frequencies -f5c index --slow5 chr22_meth_example/reads.blow5 chr22_meth_example/reads.fastq -f5c call-methylation --slow5 chr22_meth_example/reads.blow5 -b chr22_meth_example/reads.sorted.bam -g chr22_meth_example/humangenome.fa -r chr22_meth_example/reads.fastq > chr22_meth_example/result.tsv +f5c index -d chr22_meth_example/fast5_files chr22_meth_example/reads.fastq +f5c call-methylation -b chr22_meth_example/reads.sorted.bam -g chr22_meth_example/humangenome.fa -r chr22_meth_example/reads.fastq > chr22_meth_example/result.tsv f5c meth-freq -i chr22_meth_example/result.tsv > chr22_meth_example/freq.tsv - #event alignment -f5c eventalign --slow5 chr22_meth_example/reads.blow5 -b chr22_meth_example/reads.sorted.bam -g chr22_meth_example/humangenome.fa -r chr22_meth_example/reads.fastq > chr22_meth_example/events.tsv +f5c eventalign -b chr22_meth_example/reads.sorted.bam -g chr22_meth_example/humangenome.fa -r chr22_meth_example/reads.fastq > chr22_meth_example/events.tsv + +#### NOTE: If you are using FAST5 format, make sure to specify --pore r10 for R10.4.1 data and --rna for RNA data. These are autodetected for S/BLOW5 in latest f5c. ``` ## Generic methylation calling workflow