Class 22: Parsing fastq files, part 1

May 18, 2020

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Session log

Luis Perez
2020-05-18 09:00:06
**Class started**
Luis Perez
2020-05-18 09:24:22
**Entering breakout rooms**
Luis Perez
2020-05-18 09:25:20
Share one new thing you learned from the 00_fastq-filesnotebook? (Reply in thread.)
Luis Perez
2020-05-18 09:25:35
What should we discuss in the main session from the 00_fastq-filesnotebook? (Reply in thread).
Polly Poll
2020-05-18 09:25:48
Poll by @Luis Perez
I would rate my understanding of the material in the 00_fastq-filesnotebook as:
😱⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ 0
🙁████████████████ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢16
😐████ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢4
🙂████ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢4
😄⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ ⁢ 0
Luis Perez
2020-05-18 09:26:04
Help! We need a TA! (reply in thread if you need a TA)
Hannah Markovic
2020-05-18 09:42:08
TA in lightest_lizard?
Mike Harms
2020-05-18 09:42:56
👍
Philip Nosler
2020-05-18 09:29:43
What is the TAGGCATG+ at the beginning of each segment of sequence?
Mike Harms
2020-05-18 09:34:04
I believe it is the barcode pair used to define the read sample. The headers have some defined fields (https://help.basespace.illumina.com/articles/descriptive/fastq-files/. The TAGGCATG+ bit is extra information put in by the sequencing core.
Philip Nosler
2020-05-18 09:35:39
Okay, thanks!
Luis Perez
2020-05-18 09:51:06
**Leaving breakout rooms**
Luis Perez
2020-05-18 10:02:38
**Class ending**