Visualization of sam file to find introns

[Dolphin22]

Hey guys

I have a .sam file from bowtie2 and I want to see if there is a high number of reads mapped on intronic sequences..
What is the fastest solution? I planned to visualize the alignment in comparison to a gff file.
But it seems to be very labourous. So, is there a tool that has a table as output where I can see how many reads are mapped to introns?

[cascoamarillo]

Hi,
To visualize sam or bam file with gff, the best option is GBrowse.
About how many reads are located in the introns; what is the gff file version (2 - 3?), something like this?:

##gff-version 3
scaffold_1	Gaze	gene	84	2328	93.4297	-	.	ID=GSADVG00000001001;Name=GSADVG00000001001
scaffold_1	Gaze	mRNA	84	2328	93.4297	-	.	ID=GSADVT00000001001;Parent=GSADVG00000001001;Name=GSADVT00000001001
scaffold_1	Gaze	UTR	84	409	1.6390	-	.	Parent=GSADVT00000001001;Name=GSADVT00000001001
scaffold_1	Gaze	CDS	410	488	1.6374	-	2	Parent=GSADVT00000001001;Name=GSADVT00000001001
scaffold_1	Gaze	CDS	552	686	13.9647	-	2	Parent=GSADVT00000001001;Name=GSADVT00000001001
scaffold_1	Gaze	CDS	742	875	9.9687	-	0	Parent=GSADVT00000001001;Name=GSADVT00000001001
scaffold_1	Gaze	CDS	939	1093	5.3854	-	1	Parent=GSADVT00000001001;Name=GSADVT00000001001

In this case you can do this (maybe not the best): use HTSeq to count the reads mapped in the gene (gene-ID) and then use the same to count the exon reads (CDS-Parent); the difference would give you a approximation (take off the UTR reads too if you have it).

I've tried different scripts (from different sources) to to show up the intron regions given a gff file like that; though the outputs weren't too good. If anyone knows a better one, please let us know.

[maubp]

You could try using Tablet for this (on Windows, Mac or Linux on your own computer). Load an assembly (SAM/BAM + reference) and then import the GFF file of features. The feature rendering is quite simple but enough to see intron/exon boundaries and compare them by eye to RNA Seq coverage.

http://bioinf.hutton.ac.uk/tablet/

http://bioinf.hutton.ac.uk/tablet/help/importing-features.shtml

GBrowse is good but intended to run on a server, and is quite a lot of work to setup. It might still be a better choice - it depends what exactly you want to do.