Versions Compared

Old Version 4

changes.mady.by.user Deatherage, Daniel E

Saved on

compared with

New Version 5

changes.mady.by.user Deatherage, Daniel E

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

Table of Contents

...

Often, the first thing you (or your boss) want to know about your sequencing run is simply, "how many reads do I have?". 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 searched 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

...

This is another example of different solutions giving the same final product, and how careful reading of documentation may improve your work. NGS data analysis is a results driven process, if the result is correct, and you know how you got the result it is correct as long as it is reproducible.

A note on versions 


Info

In our first tutorial we mentioned how knowing what version of a program you are using can be. When we loaded the the cutadapt module we didn't specify what version to load. 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 module system or the program's help files

Code Block
languagebash
titleStill not sure?
collapsetrue
module spider cutadapt

cutadapt --version

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 v2.10 being released on April 22nd this year.

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

The biggest reason is that someone at tacc has to go through a process of noticing that there is a new version, figuring out if all of the changes are compatible with tacc, installing it, and then fielding questions and problems from users who were used to using the old version and have problems with the new version somehow.

The next reason is that the existing version works, and if you read through some of the recent changes, are very small and do not effect the function of the program very much.


Together, this is why I encourage you to make note of what version of the programs you use when you use them (primarily by loading modules complete with the versions in your .bashrc file), and to consider installing programs yourself when appropriate (as is discussed in the advanced trimmomatic tutorial for read trimming).

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.

...