<commit_before>---
layout: post
title: June Bits
date: ‘2022-06-15’
categories:
tags:
---

This is a running daily of all the stuff done in June.

---

**June 17**

Trying epidiverse / snp







---

June 16

Plan to look at Oly paper revisions and push ceabigr a bit.

Tried BS-snper Oly -> too many chromosomes.

Trying to tackle kallisto in ceabigr.; got it.

Ran the following to try to get conversion efficiency on Oly work
```
#!/bin/bash
## Job Name<commit_msg>add a bit on epidiverse<commit_after>---
layout: post
title: June Bits
date: ‘2022-06-15’
categories:
tags:
---

This is a running daily of all the stuff done in June.

---

**June 17**

Trying epidiverse / snp

What a mess.

BS-SNPer not doing well with Oly v82 (100000k and bigger / 32 contigs). Not sure of issue.





---

**June 16**

Plan to look at Oly paper revisions and push ceabigr a bit.

Tried BS-snper Oly -> too many chromosomes.

Trying to tackle kallisto in ceabigr.; got it.

Ran the following to try to get conversion efficiency on Oly work
```
#!/bin/bash
## Job Name
{'fraction_non_alphanumeric': 0.09943181818181818, 'fraction_numerical': 0.032196969696969696, 'mean_word_length': 3.0343511450381677, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6926893', 'n_tokens_mistral': 405, 'n_tokens_neox': 354, 'n_words': 162}