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SFA module explanation
This module provides a brief overview on the new functional impact predictions. Additions to this module are planned to allow the automated generation of publication quality figures.
A cInDel event is the combination of two or more InDels, which compensate the frameshift(s) caused by each other. Since stop codons could by chance after the first frameshift, the distance between compensating frameshifts is often very short.
This module can be started with navip.py through the --sfa option. It needs the VCF file produced by NAVIP to access the NAV1 information inside the INFO column. The out path to an existing folder will be used to place all output files in a single directory.
The option --format defines which of the image formats (PNG, PDF, PS, EPS, or SVG) will be used. The string after --format will be handled like a comma separated list and generates an image file for each specified format.
The option --ecc disables the modulo operation while searching for cIndels. Without the modulo operation in place the only cInDels found will be compensated through the opposite: insertions compensated by deletions and deletions compensated by insertions, respectively.
The option --max_x_axis_bpr is the parameter for the maximal X-axis label in the sfa-cInDel pictures. The complete data will still be in the files. This will improve the picture clarity.
Every run will produce at least eight output files (2019-03-25). Without using the --ecc option, files will be named like this:
transcripts_isoform_cInDels.svg
#image
transcripts_isoform_cInDels.txt
transcripts_isoform_cInDels_TIDs.txt
transcripts_isoform_cInDels_TIDs_detailed.txt
transcripts_isoform_cInDels_TIDs_detailed_sorted_by_TID.txt
transcripts_unique_cInDels.svg
# image
transcripts_unique_cInDels.txt
transcripts_unique_cInDels_TIDs.txt
The possibility for genes to have many transcripts/isoforms led to a higher number of cases for cInDel events. This is the reason for splitting a part of the output into "unique" (statistics on the gene level) and "isoform" (statistics on the transcript level). The files transcripts_isoform_cInDels.txt and transcripts_unique_cInDels.txt will look like this (TAB separated):
#transcripts with X indels
#distance_between_compensation_fs X=2 X=3 X=4 X=5
1 30 0 0 0
2 59 0 0 0
3 115 0 0 0
4 68 0 0 0
5 26 0 0 0
6 35 3 0 0
[...]
The first two rows are a shortened description of the format. The first column is the distance_between_compensation_fs value. It is the maximal absolute distance between the the new CDS positions of all cInDels. A distance of 1 means all InDels are directly next to each other, while a distance of 2 means one unaffected base between the InDels. The "X=" values are the numbers of cInDels involved in the cInDel event. The data row:
6 35 3 0 0
indicates, that with a max distance of 6 between the cInDels there are 38 transcripts affected. The X=2 column means the 35 affected transcripts are having a cInDel set of two and there are 3 cases in which three cInDels together compensate the frameshift. In this case the distance is measured between the first and the last cInDel.
The files transcripts_isoform_cInDels_TIDs.txt and transcripts_unique_cInDels_TIDs.txt will look like ths:
#Header: > <bp> <quantity of involved InDels for one compensating InDel (cInDel) event>
#Data line: <tid>,<tid>....<tid> max 10x per line
>1 2
AT1G22060.1,AT1G22060.2,AT1G22370.2,AT1G31400.1,AT1G34575.1,AT1G37140.1,AT1G37140.2,AT1G52000.1,AT1G52000.2,AT2G24690.1
AT2G24690.2,AT2G29120.1,AT2G29490.1,AT3G11010.1,AT3G11010.2,AT3G11010.3,AT3G11010.4,AT3G11010.5,AT3G11010.6,AT3G50060.1
The file transcripts_isoform_cInDels_TIDs_detailed.txt looks like this:
#Header: > <bp> <quantity of involved InDels for one compensating InDel (cInDel) event>
#Data line: <tid|cInDel-event 1| cInDel-event2| ....>
#cInDel-event:<Chr>,<Pos>,<CDS-Pos>,<frameshift-value>;<Chr>,<Pos>,<CDS-Pos>,<frameshift-value> [...]
#frameshift-value: integer values: deletion: -1,-2 bases; insertion: 1,2 bases
>3 2
AT1G06220.1|Chr1,1900873,350,2;Chr1,1900874,353,1
AT1G06220.2|Chr1,1900873,350,2;Chr1,1900874,353,1
AT1G27170.1|Chr1,9436258,1442,-1;Chr1,9436262,1445,-2|Chr1,9436894,1994,2;Chr1,9436895,1997,-2
AT1G27170.2|Chr1,9436258,1442,-1;Chr1,9436262,1445,-2|Chr1,9436894,1994,2;Chr1,9436895,1997,-2
The same information can be found inside transcripts_isoform_cInDels_TIDs_detailed_sorted_by_TID.txt, but more compact while searching for all events inside one transcript:
#Data line: <tid>,<quantity cindel-events>|<max_bpr>,<InDel_quantity>,cInDel-event 1|<bpr><InDel_quantity>,cInDel-event2| ....>
#cInDel-event:<Chr>,<Pos>,<CDS-Pos>,<frameshift-value>;<Chr>,<Pos>,<CDS-Pos>,<frameshift-value> [...]
AT1G23250.2,1|79,2,Chr1,8255303,458,2;Chr1,8255229,537,1
AT1G27180.1,5|12,2,Chr1,9440149,285,1;Chr1,9440154,297,2|12,2,Chr1,9440161,309,1;Chr1,9440166,321,-1|1110,2,Chr1,9441673,861,-2;Chr1,9442871,1971,-1|5,2,Chr1,9443928,2867,1;Chr1,9443929,2872,-1|154,2,Chr1,9444900,3842,-2;Chr1,9445056,3996,-1
The second entry is a transcript with five different cInDel events, separated by "|". The first value, the <max_bpr> is the maximal distance from the first to the last InDel of this event. The second value is the number of involved InDels, followed by chromosome, position, CDS position and the frameshift value. The insertion of one or two additional nucleotides are shown as 1 or 2, respectively. The deletion of one or two nucleotides are shown as -1 and -2, respectively.