Calculating read lengths - SOLiD

naluru · 01-13-2011, 06:33 PM

I am working with SOLiD data and have trimmed reads. I am trying to calculate the length of the reads and their number. I have seen several publications where they have shown these details.

My question is, do you calculate them using linux commands? or is there any other efficient way to do it. Any hints will be highly appreciated.

Thank you

colindaven · 01-26-2011, 04:57 AM

If you have base space fasta files have a look at the tool Galaxy online. There are tonnes of other tools which should do this for you. R may also be useful for you.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Mixed read lengths in TopHat input file	shurjo	Bioinformatics	13	11-01-2012 04:46 AM
amplicon read lengths	SeqNerd	Ion Torrent	2	06-08-2011 10:50 PM
Platform comparison of read lengths	ryantkoehler	General	0	10-05-2009 08:37 AM
How to visualise alignments with different read lengths?	lindseyjane	Bioinformatics	5	09-17-2009 01:27 AM
Pacific Bio releases some details on SMRT Sequencer read lengths, library prep	ECO	The Pipeline	6	10-15-2008 12:54 PM

01-13-2011, 06:33 PM	#1
naluru Member Location: Woods Hole, Massachusetts Join Date: Jul 2010 Posts: 16	Calculating read lengths - SOLiD I am working with SOLiD data and have trimmed reads. I am trying to calculate the length of the reads and their number. I have seen several publications where they have shown these details. My question is, do you calculate them using linux commands? or is there any other efficient way to do it. Any hints will be highly appreciated. Thank you

01-26-2011, 04:57 AM	#2
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	If you have base space fasta files have a look at the tool Galaxy online. There are tonnes of other tools which should do this for you. R may also be useful for you.