We want to complement our indels study in primary cells after CRISPR/CAS9. We are looking for a cheaper way to identify large deletions in our targeted loci. Normal Tide/ice analyses only consider >50 bp/>30bp window due to decombolution limitations. Is it possible to estimate larger deletions in long amplicons directly from the Fastq files of nanostring sequencing, such as the ones provided by plasmidsaurus or similar services? Anyone has experience trying to deal with this large deletions in mammal cells.
Thanks in advance for any tips on this!
J
The standard Plasmidsaurus amplicon service is meant for homogeneous molecular samples since it uses tagmentation to break the amplicon into pieces. You can ask [email protected] about sequencing long amplicons that may have a variety of indels in the different molecules in the sample, since there is a custom service that uses end-ligation to prepare the library and every read is a full-length sequence of that molecule.
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