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bsbdenovo-datasets2 [2017/11/21 11:13]
telatina
bsbdenovo-datasets2 [2020/02/07 09:51]
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-====== More datasets ====== 
  
-This session will list and introduce a range of **whole genome shotgun** experiments. They all are //​Escherichia coli// isolates (different strains, unfortunately),​ but sequenced with different platforms: 
-  - Roche 454 (and 454 Junior) 
-  - Thermo IonTorrent (Proton) 
-  - Illumina (MiSeq) 
-  - Oxford Nanopore (MinION) 
-  - Pacific Biosciences (PacBio) 
- 
-**Note** that these datasets have been downloaded from a public repository called **Short Reads Archive** hosted by the NCBI. It's a useful source of published and publicly available NGS datasets, that can be very useful to test pipelines or add "​controls"​ to your analyses. 
- 
-===== Where are these datasets ===== 
-The general path to explore these datasets is ''/​bsb/​denovo/​datasets/''​. 
- 
-==== What's inside this directory? ==== 
-Let's simply list the content of the directory with the datasets: 
-<code bash> 
-ls -l /​bsb/​denovo/​datasets/​ 
-</​code>​ 
- 
-The output is something like: 
-<​code>​ 
-total 28 
-drwxrwsr-x 2 ubuntu ubuntu 4096 Nov 21 17:45 454 
-drwxrwsr-x 2 ubuntu ubuntu 4096 Nov 21 17:48 454JR 
-drwxrwsr-x 2 ubuntu ubuntu 4096 Nov 21 17:45 illumina 
-drwxrwsr-x 2 ubuntu ubuntu 4096 Nov 21 17:49 ionproton 
-drwxrwsr-x 2 ubuntu ubuntu 4096 Nov 21 17:45 mixed 
-drwxrwsr-x 2 ubuntu ubuntu 4096 Nov 21 17:51 nanopore 
-drwxrwsr-x 2 ubuntu ubuntu 4096 Nov 21 17:51 pacbio 
-</​code>​ 
- 
-Basically a set of directories reminding us which platform generated the dataset. If we wanted to list all files with ''​.fastq''​ as extension contained in the directory //and its subdirectories//​ we could simply use the **find** command: 
-<code bash> 
-find /​bsb/​denovo/​datasets/​ -name "​*.fastq"​ 
-</​code>​ 
- 
-==== How many sequences in each dataset? ==== 
-Last week we introduced the [[http://​bioinf.shenwei.me/​seqkit/​|SeqKit]] package to analyse and manipulate FASTA and FASTQ files. 
-The ''​seqkit stats''​ program quickly counts the reads, giving also the total amount of bases and maximum, average and minimum read length. 
- 
-Let's try analysing the output of the good old 454 run: 
-<code bash> 
-seqkit stats /​bsb/​denovo/​datasets/​454/​SRP001673.fastq 
-</​code>​ 
-We totally have about 95Mbp, that for an //E. coli// genome means we produced a 20X coverage shotgun. Not that bad! 
- 
-==== How do reads look like? ==== 
-Different dataset vary. A simple way to have a look is using the ''​less''​ command. Remember that when using ''​less''​ you can interact with keystrokes (arrows, page up/down, and finally ''​q''​ to exit!). 
-Example: 
-<code bash> 
-less -S /​bsb/​denovo/​datasets/​454/​SRP001673.fastq 
-</​code>​ 
-We can use the ''​-S''​ parameter to avoid word wrap, and keep the sequences in one line (use left/right arrows to scroll).