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NCGG-MGC / IMSindel

IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis
https://www.nature.com/articles/s41598-018-23978-z
MIT License
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Output corrected chromosome as fasta #7

Open sarahshah opened 5 years ago

sarahshah commented 5 years ago

This is not an issue, but it'd be convenient if there was a feature to output different versions of the whole corrected chromosome as fasta files. The current flag --output-consensus-seq outputs only segments of the corrected chromosomes that contain indels.

holrock commented 5 years ago

Thank you for your comment. As we do not understand what kinds of output data you want exactly, could you tell me the detailed format and why the format is necessary?

sarahshah commented 5 years ago

Currently, when I input a 3-Mbp long contig (from a Canu assembly of Nanopore long reads) and a sorted bam file of short reads (Illumina) mapped to the contig (using Bowtie2), with the flag --output-consensus-seq, I get a report saying there were 304 possible indels. In addition, I also get 304 fasta files that I assume contain corrected versions of each indel, made up from short reads aligned together into a consensus sequence. I was wondering if it was possible to output the whole corrected contig as a fasta file including the uncorrected sequences, i.e. regions where no indels were found.

On Mon, 17 Dec 2018, 11:28 a.m. holrock <notifications@github.com wrote:

Thank you for your comment. As we do not understand what kinds of output data you want exactly, could you tell me the detailed format and why the format is necessary?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/NCGG-MGC/IMSindel/issues/7#issuecomment-447704096, or mute the thread https://github.com/notifications/unsubscribe-auth/Ag4lsiwShyRYimjBnZLZVYn7t8qdb3Qbks5u5wFLgaJpZM4ZReyq .