Swaraj Basu

Attaching the file for your usage Selina, the link seems to be working right now. You could also download it from here https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz

Hi Daniel, I missed this comment in the dicussion. Please find a potential solution here https://sourceforge.net/p/mitosalt/discussion/general/thread/71867dc46f/#dc44 -Regards Swaraj

Hello Halima and Valentin. Unfortunately I am not able to maintain this repo since the past year and a half, hence the delay in my responses. Apologies. MitSalt currently generates a PERL hash oject to process the alignments generated by last. In regular sequencing we would have less mitochondrial origin reads and hence the hash object is not large enough to occupy entire memory. However in enriched sequencing, a due to a large number of reads, the hash object creation step is killed. Here I would...

Good to know Eliezer that version update of plotrix solved the issue. I am sure your input will help others as well who are using MitoSAlt. Thank you Swaraj

Hi Michael, Immensely sorry for my late replies. I am not actively maintaining MitoSAlt as of now and due to several other commitments taking up my time there is a delay. If you'd like to use hg38 aligned BAM, then it should not hinder the other steps as the unaligned/MT aligned reads will be re-aligned to the MitoSAlt MT genome fasta file stored in genome/human_mt_rCRS.fasta thus negating any bias due to a difference in genome version. -Regards Swaraj

Hello Bengsiu, A few others are also facing an issue running MitoSAlt on single end reads, where the plot and tsv files are not generated. Could you please share your experience with the issue and how you could get it to work. Is this a MitoSAlt_SE specific problem? -Regards Swaraj

Hello Bengsiu, A few others are also facing an issue running MitoSAlt on single end reads, where the plot and tsv files are not generated. Could you please share your experience with the issue and how you could get it to work. Is this a MitoSAlt_SE specific problem?

Hi Tomasz, Could you please refer to my answer to Joan above and confirm if the R packages are installed and output from the PERL part of the pipeline is generated that is tab/tag.tab which is followed by .breakpoint, .bed, .cluster. Please let me know what are your observations. Thanks Swaraj