diff --git a/README.md b/README.md index 70cabe6a..e9153ba0 100644 --- a/README.md +++ b/README.md @@ -280,8 +280,9 @@ This will generate **diffIdx**, **info**, **split**, and **taxID_list** and some ## Example +> The example here was detecting SARS-CoV-2 variant-specific reads, but has changed since the pre-built DB no longer contains the variant genomes. -Classifying RNA-seq reads from a COVID-19 patient to identify the culprit variant. +Classifying RNA-seq reads from a COVID-19 patient. The whole process must take less than 10 mins using a personal machine. #### 1. Download RefSeq Virus DB (1.5 GiB) @@ -293,7 +294,7 @@ metabuli databases RefSeq_virus OUTDIR tmp ``` fasterq-dump --split-files SRR14484345 ``` ->- Download SRA Toolkit containing `fasterq-dump` [here](https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit) +> Download SRA Toolkit containing `fasterq-dump` [here](https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit) #### 3. Classify the reads using metabuli ``` metabuli classify SRR14484345_1.fq SRR14484345_2.fq OUTDIR/refseq_virus RESULT_DIR JOB_ID --max-ram RAM_SIZE @@ -301,10 +302,6 @@ fasterq-dump --split-files SRR14484345 #### 4. Check RESULT_DIR/JOB_ID_report.tsv Find a section like the example below ``` - 92.1796 510194 489403 no rank 2697049 Severe acute respiratory syndrome coronavirus 2 - 3.4290 18979 18979 subspecies 3000001 SARS-CoV-2 beta - 0.2488 1377 1377 subspecies 3000003 SARS-CoV-2 gamma - 0.0459 254 254 subspecies 3000000 SARS-CoV-2 alpha - 0.0284 157 157 subspecies 3000004 SARS-CoV-2 omicron - 0.0043 24 24 subspecies 3000002 SARS-CoV-2 delta + 92.2331 510490 442 species 694009 Severe acute respiratory syndrome-related coronavirus + 92.1433 509993 509993 no rank 2697049 Severe acute respiratory syndrome coronavirus 2 ```