plotting read length distribution of Single End data

Question

[Meghan.T]

So I have a rather obvious question that's been bugging me for few days. I am trying to plot read length distribution of a Single end sequencing data, essentially to get a better understanding of the fragment length distribution. With paired end data I see there are tools like picard [1]CollectInsertSizeMetrics that plot the fragment length distribution. I am looking to produce a figure like below but don't know what tool to use.

Answer 1

[GenoMax]

You can't determine fragment length from single end sequencing data since you are missing information about sequence at 3'-end of that fragment (with one exception: if your insert sizes are shorter then the length of sequencing then even with a single end read you will see the sequence of adapter on the 3'-end and thus should be able to determine fragment/insert size).

I am trying to plot read length distribution of a Single end sequencing data,

Read length distribution is something different. You can use a tool from BBTools to get the length/count list, which you can then plot.

$ reformat.sh -Xmx4g in=test.fastq lhist=readstats.txt

$ more readstats.txt 
#Length Count
156     1
175     1
203     1
221     1
233     1
242     1
246     1
266     1
267     1
273     1
274     1
278     1
279     2
282     1
286     1
292     1
297     1
298     3
299     6
300     11
301     62