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Old 10-16-2013, 07:42 AM   #1
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Default how to detect contamination or sample preparation artifacts in sequencing results


Is there any tool (apart from fastQC) to detect all primers/adapters(contaminants basically) in my raw fastq file that needs to be removed before mapping?
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Old 10-16-2013, 08:01 AM   #2
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Old 10-17-2013, 03:13 AM   #3
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Originally Posted by JackieBadger View Post
Thanks. I start using this and now it complaints about libraries.

No search libraries were configured at /Downloads/fastq_screen_v0.4.2/fastq_screen line 119.

I assume it refers to the contamination list. I have the cocntaminant file from the fastQC but it is not clear to me where to mention this list.

I use the following line in my conf file.

DATABASE Adapters /Volumes/bowtie2_index/

Can you please advise if by library it means contamination list and where i should mention the libraries?
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adapter, contamination, fastq, mapping, trimming

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