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Old 07-09-2012, 06:54 AM   #1
figo1019
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Default Illumina read trimming

Hi,

I am a newbie in NGS analysis so may be it is a basic question. I have been given fastq files of paired end reads of 100 bp by the company and in the read me file they have asked me to trim the initial 6 base pairs from all the sequences. So i want to know if some one knows why they have asked me to do this ... are these because these are barcode information or the index sequence or adaptors?

Regards
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Old 07-09-2012, 09:43 AM   #2
geneart
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hello figo1019,
mostly they would want the adaptors trimmed , but then they have asked u to trim only the first 6 bases. But if you had adaptors as in case of illumina they would be at both ends and a little longer in length(more than 6bases).
It also depends on what NGS platform they have used?
so not completely sure .......
geneart.
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Old 07-09-2012, 09:46 AM   #3
westerman
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Depends on what technology was used to produce the fastq files. At 100 bp it is likely that these came from Illumina. In which case the index and adapters would already be stripped off. Perhaps the read quality is poor? But ... heck ... who really knows the mind of "the company".
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Old 07-12-2012, 09:38 AM   #4
sklages
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Quote:
Originally Posted by figo1019 View Post
Hi,

I am a newbie in NGS analysis so may be it is a basic question. I have been given fastq files of paired end reads of 100 bp by the company and in the read me file they have asked me to trim the initial 6 base pairs from all the sequences. So i want to know if some one knows why they have asked me to do this ... are these because these are barcode information or the index sequence or adaptors?

Regards
Why don't you just ask "the company"?

Just my 2p ;-)
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