One of the basic steps in RNA-seq analysis is to plot a length ditribution. There are several ways of doing it.

Using unix commands

link in Biostars

awk 'NR%4 == 2 {lengths[length($0)]++} END {for (l in lengths) {print l, lengths[l]}}' file.fastq

First part of awk commands tell the program to pick up the second line group by each 4 lines. And second part saves length of that line as a component of lengths matrix. And the last part is that at the end of the process, print lengths matrix showing length and count.

cat reads.fastq | awk '{if(NR%4==2) print length($1)}' | sort -n | uniq -c > read_length.txt

With this command, you can save lengths matrix as a file. This time you can put sort and uniq to make sure that the list are sorted and has only unique lengths.

Using BBMap utilities

readlength.sh in=reads.fq out=histogram.txt

This is really fast and this program can handle multiple formats of read files such as fastq, fastq.gz, fasta, sam, bam

Text manipulation tools

link

sort

sort -t : -k 4 -k 1 -g /etc/passwd | more

-t is the option for the separator chacter, -k 4 means to select 4th column for indexing, -k 1 means to use 1st column after sorting by 4th column. -g is used if the numerical sorting is not working. -r is for reverse sort.

join

Will put two lines together assuming they share at least one common value on the relevant line. It won’t print lines if they don’t have a common value.

cut

cut -d ':' -f 1,7 /etc/passwd

-d is for the separator character, -f is used to select columns.

ispell/aspell

chcase

cat fileName.txt | tr '[A-Z]' '[a-z]'  > newFileName.txt

chcase is used for converting lower case chacters to upper case characters, or vice versa. and it can be substituted by the above tr command.

fmt

paste

paste file1.txt file2.txt

You can see lists of two files side by side.

expand

unexpand

uniq

• -c - count the number of occurances of each duplicate
• -u - list only unique entries
• -d - list only duplicate entries

tr (translation)

cat some_file | tr '3' '5' > new_file

This commands write a new_file with 5 where 3 locates before. tr finds all cases and replaces with new character.

nl

the number lines tool