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Table of Contents

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Often, the first thing you (or your boss) want to know about your sequencing run is simply, "how many reads are there?". For the $BI/gva_course/mapping/data/SRR030257_1.fastq file, the answer is 3,800,180. How can we figure that out?

The grep (or Global Regular Expression Print) command can be used to determine the number of lines which match some criteria as shown above. Above we used it to search for:

  1. anything from the group of ACTGN with the [] marking them as a group
  2. matching any number of times *
  3. from the beginning of the line ^
  4. to the end of the line $

Here, since we are only interested in the number of reads that we have, we can make use of knowing the 3rd line in the fastq file is a + and a + only, and grep's -c option to simply report the number of reads in a file.

Code Block
languagebash
titleCan you use the information above to write a grep command to count the number of reads in the same file?
collapsetrue
grep -c "^+$" $BI/gva_course/mapping/data/SRR030257_1.fastq

...

Info

In our first tutorial we mentioned how knowing what version of a program you are using can be. When we installed the the cutadapt package we didn't specify what version to install. Can you figure out what version you used, and what the most recent version of the program there is? .

Expand
titleHow to figure out the currently installed version

try using the program's help files, or conda's list function

Code Block
languagebash
titleStill not sure?
collapsetrue
cutadapt --version
conda list
conda list cutadapt

Note that all 3 of the above commands will give you the same answer: 1.18

Figuring out the most recent version is a little more complicated. Unlike programs on your computer like Microsoft Office or your internet browser, there is nothing in an installed program that tells you if you have the newest version or even what the newest version is. If you go to the programs website (easily found with google or this link), the changes section lists all the versions that have been list with v3.4 being released on March 30th of this year.

Expand
titleTake a moment to think about click here for information regarding why there might be is such a big discrepancy before clicking here for the list of possible reasons I put together.large discrepancy

If you were to look at the labels section of https://anaconda.org/bioconda/cutadapt you would see that both v3.4 and 1.18 

This won't be the last time we mention different

v1.18 are available. Since we didn't specify a version, conda tried to figure out what would work best. If you were to play around with removing the cutadapt package and attempt to force v3.4 to be installed you would eventually come to find that there is a conflict between the python version we have installed (3.7.10) which is higher than the allowed python versions available with V3.4. Cutadapt version 1.18 however does not have such requirements for installation and therefore was installed as the only available option. 

To install the 3.4 version of cutadapt via conda, we would have to explicitly specify both the version of cutadapt that we wanted (3.4) as well as a compatible version of python (less than 3.7). Given that the version 1.18 did the job, it is not likely to be worth the effort to update the cutadapt version. 

This won't be the last time we mention different program versions.

Optional Exercise: Improve the quality of R2 the same way you did for R1.

Unfortunately we don't have time during the class to do this, but as a potential exercise in your free time, you could improve R2 the same way you did R1 and use the improved fastq files in the subsequent read mapping and variant calling tutorials to see the difference it can make in overall results.


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