Question: How to remove primers from a Roche 454 sff file
0
gravatar for pingEde
2.8 years ago by
pingEde20
European Union
pingEde20 wrote:

Good morning,

I am implementing a pipeline for Roche 454 Junior and I have few questions, I hope that someone could help me :)

I do not know the structure of reads that are in the SFF file, I think that they are composed by MID- Primer 1- Sequence - Primer 2- MID, it is wrong? Primer1 and Primer2 are different or same?

Could you suggest a good tool to remove primers?

Thank you in advance for your attention!

Best regards

 

454roche primer tool sff reads • 1.1k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by pingEde20

Thank you for your response, I have already converted the file to fast with a tool of Galaxy, I have divided the file .fasta according MIDs and now I have to trim primer... It is my problem, because I am not sure of the structure of the read and what is happened if the amplicon sequencing is longer than the final reads and it is possible that the end of the read (3') is incomplete. Thank you for your help

ADD REPLYlink written 2.8 years ago by pingEde20
1

Mothur can trim the primers as well. It is easy to see the primers, they are at the beginning of each read.

Note that you don't even always need to remove primers for analysis methods to work. And yes the end of the amplicon may be missing, that's not necessarily a problem either. It all depends on the quality of data, the statements that you wish to make off of them. 

ADD REPLYlink written 2.8 years ago by Istvan Albert ♦♦ 77k

Thank you very much for you response, could you suggest me where can I download reference genome (human hg19) to use in tool of mapping?
Thank you in advance for your help!

ADD REPLYlink written 2.8 years ago by pingEde20
1

see this https://www.biostars.org/local/search/page/?q=download+human+genome

ADD REPLYlink written 2.8 years ago by Istvan Albert ♦♦ 77k
The MID isn't in the readsequence I think.
ADD REPLYlink written 2.8 years ago by Zaag620

Thank you for your response, I have verified that the MID is present in the read :)

ADD REPLYlink written 2.8 years ago by pingEde20
2
gravatar for Istvan Albert
2.8 years ago by
Istvan Albert ♦♦ 77k
University Park, USA
Istvan Albert ♦♦ 77k wrote:

Convert the file to fasta then operate on it with other quality control tools.

See mothur or other tools for an easy to use sff converter.

ADD COMMENTlink written 2.8 years ago by Istvan Albert ♦♦ 77k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1406 users visited in the last hour