split, merge, reformulate assembly_visualization.md #7
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…ute/nvi-documentation into evfi_split_move_assembly_visualization
docs/source/tutorials/Visualisation_assembly_reads_pileup_IGV.md
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docs/source/tutorials/Visualisation_assembly_reads_pileup_IGV.md
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docs/source/tutorials/Visualisation_assembly_reads_pileup_IGV.md
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| ## 2. Example: Using IGV with reads mapped to its own assembly | ||
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| We have assembled reads and annotated using Bifrost pipeline. The data for today's practical are found in `/cluster/projects/nn9305k/tutorial/20210412_mapping_visualization/visualisation_files` |
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Done - but hanging on data is/are ... RRR
so "read" (on the fly) https://www.theguardian.com/news/datablog/2010/jul/16/data-plural-singular
Ok to you are ?
docs/source/tutorials/Visualisation_assembly_reads_pileup_IGV.md
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| ```bash | ||
| # transfering from SAGA | ||
| rsync -rauPW <user_name>:<source_folder> <destination_folder> | ||
| ``` |
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Remove this, rather refer to a different file for that info
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ok, we have to merge the tutorial for file transfer then ... so created a file "transfering_files.md" - so we need to fill it
or change it to something done (did not find something only about file transfer)
docs/source/tutorials/Visualisation_assembly_reads_pileup_IGV.md
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| Read mapping is aligning each of your reads to a/the matching locus on a longer sequence. | ||
| This longer sequence can either be the isolate assembly, or an assembly of a related isolate (eg. a reference isolate for the group of isolate under study). | ||
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| You could think of read mapping as a simulation of local hybridization of your reads to the genome, at a loci where it fits well enough to hybridize. Usually few mismatches are allowed (think about the consequences). A portion of the reads may map to several loci in your genome (ie. in repeated regions). |
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at a locus
Usually a few mismatches
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Maybe add that things on the ends might not match, and maybe clipping?
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Added soft and hard clipping - please review
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ok - had corrected above, like better at
| mkdir mapping | ||
| cd mapping | ||
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| rsync -rauPW /cluster/projects/nn9305k/tutorial/20210412_mapping_visualization/mapping_practical/* . |
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This page needs to be made. Removed this part - made a link (commented above) so has to be written
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updated - please see if changes satisfactory. |
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Are people still working on this or is it stale? |
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Hum ... I think we did . This one is on stale for now at least
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Please have a review if this is satisfactory
Splitted assembly_visualization.md from BioInfoTraining.
Rechecked path on Saga, modified the organisation so each mini tutorial can be independent
check also that reference to the other tutorial work