Tag: segemehl

How does the arrangement of references influence mapping results?

Hi All, I’m currently conducting tests involving artificial reads with varying proportions of mutations and their impact on mapping results using segemehl v. 0.3.4. During my experimentation, I observed that certain reads, whose origin I am already aware of, are not aligning correctly to the intended reference. The reference sequences…

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nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs | BMC Bioinformatics

Sanger HL, Klotz G, Riesner D, Gross HJ, Kleinschmidt AK. Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc Natl Acad Sci. 1976;73(11):3852–6. doi.org/10.1073/pnas.73.11.3852. Article  CAS  Google Scholar  Arnberg AC, Van Ommen G-JB, Grivell LA, Van Bruggen EFJ, Borst P. Some yeast mitochondrial RNAs…

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Segemehl -D option doesnt work for allowing differences

Segemehl -D option doesnt work for allowing differences 0 I am trying to map short some specific short reads (19~20nts) against long reads of a fasta file (F1.fasta). I used Segemehl tool and indexed the F1.fasta file (long reads) and then used the command line below to perform the alignment:…

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