Hi all,
I have NGS data from a patient: Genomic DNA fragments ranging from 300-600bp sequenced on the MiSeq (2x250bp reads) prepared with SureSelect sample prep/target enrichment.
The DNA was enriched for a 4Mb region, but I have focussed in on a smaller anomaly and need a way of pulling out data from one small and specific area. Basically, I want to line up all the reads that contain a certain 37bp sequence and reject everything else.
So far I have tried two bits of software:
Nextgene - great for big alignments but not good for this task as I can't specify this small a region to align my data to
Sequencher - this should be able to do it in theory but can't seem to handle the amount of data I'm asking it to align and crashes
Would greatly appreciate all help and suggestions for what software I could try.
Best wishes,
Claire
I have NGS data from a patient: Genomic DNA fragments ranging from 300-600bp sequenced on the MiSeq (2x250bp reads) prepared with SureSelect sample prep/target enrichment.
The DNA was enriched for a 4Mb region, but I have focussed in on a smaller anomaly and need a way of pulling out data from one small and specific area. Basically, I want to line up all the reads that contain a certain 37bp sequence and reject everything else.
So far I have tried two bits of software:
Nextgene - great for big alignments but not good for this task as I can't specify this small a region to align my data to
Sequencher - this should be able to do it in theory but can't seem to handle the amount of data I'm asking it to align and crashes
Would greatly appreciate all help and suggestions for what software I could try.
Best wishes,
Claire
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