Hi, it sounds like you question is related to DNA sequencing, not proteomics. The TPP tools are designed for mass spectrometry proteomics, not for DNA/RNA sequencing. Let me know if I’ve misunderstood.
*From:* [email protected] <[email protected]> *On Behalf Of *Tuan Anh Nguyen Van *Sent:* Sunday, January 28, 2024 10:32 AM *To:* spctools-discuss <[email protected]> *Subject:* [spctools-discuss] How to assess quality of assembly of unmapped reads ? Hello everyone, I am going to construct the rice pangenome based on an iterative assembly approach. Based on this approach, I am planning to use paired-end read sequencing data. I will map the paired-end reads to the reference genome and extract the unmapped reads. Then, I will perform the de novo assembly for extracted unmapped reads into novo contigs. When I finish assembling unmapped reads, I am going to check the contamination and redundant contigs in my assembled sequence and remove these contaminated sequences before I add these novo contigs into the pangenome. I plan to use FCS-GX to detect the contamination. The newly assembled sequenced will be added to the current reference genome to generate the entire pangenome. But I am not clear, *how to assess the quality of the assembly of unmapped reads ?* -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/f0701d82-81b9-4f58-b87e-d27dce0bc573n%40googlegroups.com <https://groups.google.com/d/msgid/spctools-discuss/f0701d82-81b9-4f58-b87e-d27dce0bc573n%40googlegroups.com?utm_medium=email&utm_source=footer> . -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/fab90143330304a272b240ed58a4b8d1%40mail.gmail.com.
