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Comment
. 2023 Dec 18;24(1):778.
doi: 10.1186/s12864-023-09883-4.

Irreproducible results and unsupported conclusions in Ahmad et al. [BMC genomics (2020) 21:656]

Francisco J Ruiz-Ruano  1   2   3 , Juan Pedro M Camacho  4
Affiliations
Comment

Irreproducible results and unsupported conclusions in Ahmad et al. [BMC genomics (2020) 21:656]

Francisco J Ruiz-Ruano et al. BMC Genomics. .
No abstract available

Keywords: B chromosomes; Genes; Genomic DNA; Normalization; Transcriptome.

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Conflict of interest statement

The authors declare not having competing interests.

Figures

Fig. 1
Fig. 1
Coverage across two genes in 0B and 1B gDNA libraries of A. correntinus. We include here the results using Bowtie2 and SSAHA2 mappings for the tars (a) and ipo11 (b) genes using the NCBI contigs as a reference. Note that, in general, coverage is 0 with Bowtie2 for the shortest exons due to not considering partially mapped reads as SSAHA2 does. By comparing the y-axis scales of both graphs within each gene, note how SSAHA2 detected about twice number of copies as Bowtie2. See fold change (1B/0B) values in our Supplementary_File_1, and coverage graphics for all genes in Supplementary_Files 2 and 3, which include the collections of 26 NCBI and the 61 EBI contigs, respectively
See this image and copyright information in PMC

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References

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    1. Ruiz-Ruano FJ, Navarro-Domínguez B, López-León MD, Cabrero J, Camacho JPM. Evolutionary success of a parasitic B chromosome rests on gene content. bioRxiv. 2019 doi: 10.1101/683417. - DOI
    1. Wratten L, Wilm A, Göke J. Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers. Nat Methods. 2021;10:1161–8. doi: 10.1038/s41592-021-01254-9. - DOI - PubMed

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