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10-16-2013, 07:42 AM
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#1 |
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Member
Location: UK Join Date: Aug 2009
Posts: 38
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how to detect contamination or sample preparation artifacts in sequencing results
Hi,
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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10-16-2013, 08:01 AM
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#2 |
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Senior Member
Location: Halifax, Nova Scotia Join Date: Mar 2009
Posts: 381
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10-17-2013, 03:13 AM
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#3 | |
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Member
Location: UK Join Date: Aug 2009
Posts: 38
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Quote:
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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| Tags |
| adapter, contamination, fastq, mapping, trimming |
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