Question: Should I generate a new Index genome in STAR for 50 base reads instead of 100 base which I had before?
0
gravatar for Rimma
11 months ago by
Rimma30
Hebrew University of Jerusalem
Rimma30 wrote:

When I was generating Ggnome Indexes file in STAR I used the parameter --sjdbOverhang 100 since my reads are 100 bp length. However, now I have 50 base reads and I wondered if I can use the same index genome for it or not?

Thanks a lot!

rna-seq alignment • 438 views
ADD COMMENTlink modified 11 months ago by caggtaagtat1.0k • written 11 months ago by Rimma30
0
gravatar for caggtaagtat
11 months ago by
caggtaagtat1.0k
caggtaagtat1.0k wrote:

As far as I know, it could be beneficial to adjust the parameter you stated accordingly.

On the other hand, I also read, that it doesn't completly disrupts your data.

Edit: let me cite the STAR manual

In case of reads of varying length, the ideal value is max(ReadLength)-1 . In most cases, a generic value of 100 will work as well as the ideal value.

So I would recalcualted the STAR index.

ADD COMMENTlink modified 11 months ago • written 11 months ago by caggtaagtat1.0k
1

The quote from the manual contradicts that recalculating the STAR index is likely to be very useful.

ADD REPLYlink written 11 months ago by Devon Ryan95k

It also states, that the ideal step, however, would be to recalculate. So, since it doesn't take that long, it could be slightly beneficial. But you are right, it seems to make no huge difference.

ADD REPLYlink written 11 months ago by caggtaagtat1.0k
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