Question: Adapters Vs Pcr Fragments
2
gravatar for ric
2.0 years ago by
ric80
ric80 wrote:

Hi,

I found the belowfew software to remove adapters:

Adapters the same like PCR fragments?

Running one of the software above would it gives me the same results like MarkDuplicates.jar?

Thank you in advance.

ADD COMMENTlink modified 21 months ago by Istvan Albert ♦♦ 39k • written 2.0 years ago by ric80
1

by the way, this is a nice collection of tools listed here

ADD REPLYlink written 2.0 years ago by Istvan Albert ♦♦ 39k
0
gravatar for Istvan Albert
2.0 years ago by
Istvan Albert ♦♦ 39k
University Park, USA
Istvan Albert ♦♦ 39k wrote:

Each of the terms means something different:

  • adapter - a known sequence appended to the DNA fragment used either to extend the fragment or tag it in a certain way
  • sequencing errors - errors introduced by the sequencing instrument
  • PCR artifacts - artificial sequences that are caused by the PCR amplification process
  • duplicates - identical sequences that may or may not be cause by error (PCR amplification included)

So you need to pick the software that does what you need.

ADD COMMENTlink written 2.0 years ago by Istvan Albert ♦♦ 39k

Thank you. What kind of software would you recommend for each term?

ADD REPLYlink written 2.0 years ago by ric80

you a have a good list to start with - remember there is no single best tool - the right answer depends on many factors, most importantly what are you able to run in the first place

ADD REPLYlink written 2.0 years ago by Istvan Albert ♦♦ 39k

What kind of terms would you recommend:

  • for SNP discovery
  • assembly

Thank you in advance.

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by ric80
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