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Mate pair linker removal #56
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@CosteaPaul, can you give me some pointers to this script @hussius is referring to ? |
For doing PhiX removal on paired-end reads (which will almost always be the case) rather than single-end, an example command would be bowtie ---solexa1.3-quals --un sample_nophiX.fastq /bubo/nobackup/uppnex/reference/biodata/genomes/phiX174/phix/bowtie/phix -1 sample_1.fastq -2 sample_2.fastq /dev/null |
I'm thinking on adding a field on run_info.yaml "filter_out_gnomes" on a per-sample basis such as: multiplex: - barcode_id: '1' barcode_type: Illumina name: BAC11 sequence: ATCACG filter_out_genomes: ecoli, phix That way the get rid of the second scenario (whole lane), and we apply it to the samples that matter. @chapmanb, we spike on phiX on sample 3, that's why this feature is needed, but I think in this way it's better generalized. In addition, it can be eventually exposed as an additional field in the ngLIMS. |
Roman; |
"filter_out_gnomes" - was that typo inspired by the approaching Christmas mood? :-) |
LOL X"D Well, you never know what you might find in those magical FastQ files ;P hussius [email protected] wrote: "filter_out_gnomes" - was that typo inspired by the approaching Christmas mood? :-) Reply to this email directly or view it on GitHub: |
A better option for mate pair linker removal would be to use a modified version of Deloxer (http://genomes.sdsc.edu/downloads/deloxer/). The modified version is written by Ino DeBruijn and handles more cases than the original Deloxer. I'll ask him to put it on GitHub.
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From Brad:
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Need to include Paul's script for mate-pair linker removal - ONLY for mate-pair runs. Perhaps as part of general screening module together with PhiX, contamination + adapter screeners.
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