[Giffredo]

I am very interested on this discussion..
Can Pysamstats give me the difference between reds (forward or reverse)?

I need a table with these informations:

Chr/position/reference_base/read_base (number or %(A,C,G,T) found in forward or reverse strand)/insertion/deletion

Example:

chr1 20 A A:30 C:20 G:0 T:0 a:0 c:0 g:0 t:0 Ins:0 del:0

IGV give me something like this when I put the arrow of the mouse over a read but I need of a table...

[dariober]

I am very interested on this discussion..
Can Pysamstats give me the difference between reds (forward or reverse)?

Use variation_strand instead of variation. From the manual (https://pypi.python.org/pypi/pysamstats)

* variation_strand - as variation but with forward/reverse strand counts

[Giffredo]

Unfortunately I cannot install pysamstat package..
So, Is it possible to reach the same results using GATK for you?.. looking at the tutorial I think it cannot discriminate the variation in one strand from the other.

[dariober]

Unfortunately I cannot install pysamstat package..

What problems do you encounter? Installation errors or permissions?
pysamstats depends on numpy and pysam which can be tricky to install but it should be possible.

[Giffredo]

I have not any idea.. I cannot install anything in this Lab. there is an expert for this and he told me that is not possible. I guess it is a problem about compatibility..

[TiborNagy]

My personal opinion:
impossible == I am too lazy

The differences between -z and -w:
-z is just a memory optimization parameter. If you reduce the zoom level, you reduce the memory usage of the process
-w The window size where the coverage will be calculated. If it is 25, it means you get coverage values for every 25 bp length slice.

As far as I know GATK can not produce stats like this.

[Giffredo]

Ok, I understood... In which way I could discriminate the splicing site osing pysamstat output?
I would see the deletion sites present on my reads and not present on the references and I would check the presence of the classic splicing site bases...
I m right or there are others easier methods?

[Giffredo]

When I insert this code

pysamstats -f x.fas --type variation_strand mapq_strand  x.sorted.bam > stat_pyout.txt&

Py gives me this error:
pysamstats: error: missing file operand

What it means?

instead using:

pysamstats -f x.fas --type variation_strand x.sorted.bam > pyout.txt&

Py works well...

What am I forgetting?

[spacup]

IGV tdf file

Hi all,

About coverage file from IGV, I generated a .tdf file with count in IGV with a bin of 25 bases.

When I visualize under IGV, I have values for exemple 145,76 for a bin.
If I multiply by 25, I obtain 3644 for this bin.

Now, when I zoom and obtain the coverage track calculated by IGV from .bam file, I see that I have about 33 reads by base so about 825 reads on the bin.

So seeing this difference, my question is : does someone know how coverage is calculted in IGV's .tdf files?

thanks!

[dariober]

When I insert this code

pysamstats -f x.fas --type variation_strand mapq_strand  x.sorted.bam > stat_pyout.txt&

Py gives me this error:
pysamstats: error: missing file operand

What it means?

instead using:

pysamstats -f x.fas --type variation_strand x.sorted.bam > pyout.txt&

Py works well...

What am I forgetting?

You should pass only one option to the argument --type. So either variation_strand or mapq_strand, not both.