Post alignment using RseQC

Question

[KVC_bioinfo]

Hello,

I am using RseQC for post alignment QC. One of the parameters, it tests is clipping_profile. I am not sure what exactly that is? Can someone help me? thank you in advance.

[James Ashmore]

Check out the clipped alignment section of this FAQ: https://davetang.org/wiki/tiki-index.php?page=SAM

[KVC_bioinfo]

Thank you very much ..

[KVC_bioinfo]

I used the RSeQC and got the results for the clipped profile. Which looks like

Position    Clipped_nt  Non_clipped_nt
Read-1:
0   606725.0    4891575.0
1   331004.0    5167296.0
2   234574.0    5263726.0
3   222180.0    5276120.0
4   211349.0    5286951.0
5   203007.0    5295293.0
6   195424.0    5302876.0
7   188784.0    5309516.0
8   181843.0    5316457.0
9   176216.0    5322084.0
10  170863.0    5327437.0
11  165385.0    5332915.0
12  159808.0    5338492.0
13  154743.0    5343557.0
14  149936.0    5348364.0
15  145272.0    5353028.0
16  140931.0    5357369.0
17  136786.0    5361514.0
18  132932.0    5365368.0
19  129166.0    5369134.0
20  125544.0    5372756.0
21  122019.0    5376281.0
22  118464.0    5379836.0
23  114996.0    5383304.0
24  111136.0    5387164.0
25  107735.0    5390565.0

I am not able to understand what exactly this is

[James Ashmore]

RseQC should produce a plot of the frequency of clipped bases at each position in your RNA-seq reads. Have you had a look at the plot?

[KVC_bioinfo]

Yes. I was trying to understand the text file it generates.