diff --git a/test/HG00119_example/README.md b/test/HG00119_example/README.md index 18b117b..a246099 100644 --- a/test/HG00119_example/README.md +++ b/test/HG00119_example/README.md @@ -44,7 +44,7 @@ and `HG00119/OUT_SRR043366/logmt.txt`. **As of September 2019** -Version 1.2 of MToolBox has been released. To test the new version you can run on this test file as follows: +Version 1.2 of MToolBox has been released. To test the new version you can run it on this test file as follows: ``` diff --git a/test/HG00119_example/run_mtoolbox_on_test_file.md b/test/HG00119_example/run_mtoolbox_on_test_file.md deleted file mode 100644 index 694341b..0000000 --- a/test/HG00119_example/run_mtoolbox_on_test_file.md +++ /dev/null @@ -1,45 +0,0 @@ -

Run MToolBox on HG00119 exome data

- - -**Download the HG00119 exomes data**: - - -``` -wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR043/SRR043366/SRR043366_1.fastq.gz -wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR043/SRR043366/SRR043366_2.fastq.gz -``` - -**When donwload is complete you should have the following md5sum:** - - -``` -md5sum *.fastq.gz -a8a41bddd06e39f184ec5f5bd851843b SRR043366_1.fastq.gz -4128bc81d768169a5ff72c3fc64a4a9a SRR043366_2.fastq.gz -``` - -**Move the file name of the paired-end fastq files into MToolBox-compatible file names. For more info about file names, please read:** [NOTE ON FILE NAMES](https://github.com/mitoNGS/MToolBox/wiki/Requirements) - - -``` -mv SRR043366_1.fastq.gz SRR043366.R1.fastq.gz -mv SRR043366_2.fastq.gz SRR043366.R2.fastq.gz -ls SRR043366.R1.fastq.gz SRR043366.R2.fastq.gz > HG00119.lst -``` - -**Run MToolBox on the HG00119 paired-end dataset:** - - -First change the full path specified in `input_path` and `output_name` arguments in the `HG00119.conf` file with your paths, and then run: - - -``` -MToolBox.sh -i HG00119.conf &> HG00119.log & -``` - -You should get a log similar to the `HG00119.log` file you find in this directory. - -Intermediate logs generated by MToolBox can be found in `HG00119/logassemble.txt`, `HG00119/OUT_SRR043366/loghumanP.txt`, `HG00119/OUT_SRR043366/loghumanS.txt` -and `HG00119/OUT_SRR043366/logmt.txt`. - -