Brent

• fix coordinate translation for more edge-cases
• fix all off-by-one errors
• adjust to work with bed.gz (as well as .d4)

Mike

• make transcript plot show only union plot by default and expand to all transcript on click
• Show CDS Exon only by default. Toggle on UTRs and Non-CDS Exons
• Sort Gene/Region Selection list
• show gene.description somewhere.
• customData should use objects instead of lists so that instead of customdata[5], it uses customdata.cdsend
• update merged transcript plot

Joe

• sort gene list by name in drop-down (taken from Mike's list)
• make initial page design with nav, anchors, plot order, aesthetics
• add sample colors to table in order to remove plot legends
• add table hover events and tie them into Depth Dist per Sample plot
• fix plotly's double-click event in region plot
• see if we can manipulate region plot to improve hover events

with large cohorts or large number of genes, serializing to json becomes the slowest part of the command-line tool.
switch to use jason instead of stdlib.

Hi Brent,

I am trying to run below command

seqcover report --genes LEPR,MC4R --fasta /gpfs/data_jrnas1/ref_data/Homo_sapiens/hs37d5/Sequences/WholeGenomeSequence/hs37d5.fa temp/*.bed.gz -r my_genes_report.html --hg19

I don't have internet access from my nodes. I think I am getting error due to that.
Do you have any suggestion about how to handle this issue?

we need a way to quickly see, within the plot, which samples have aberrant coverage.

When a user changes the metric for the heatmap to CDS bases below 7 the color scale essentially inverts. Blue becomes well covered and yellow low covered. I think we should consider either flipping the colors such that blue remains the color of interest within the plot or at a minimum add a header in the dropdown that informs the user of this swap.

we don't show the chromosome of each gene anywhere.

Hi everyone,

I've been testing seqcover tool with one sample coverage file processed by mosdepth in *.bed.gz format. This sample is from a WES experiment. I run the next command and it gave me an error:

${seqcover} report --genes BRCA1 --fasta ${fasta} ${input}/sample.bed.gz -r ${outfile} --hg19

[seqcover] read 1 sample coverage files
17 41195811 41277881
strutils.nim(1087) parseInt
Error: unhandled exception: invalid integer: CEX-chr17-41196311-41197870 [ValueError]

It looks for BRCA1 coordinates on my BED file but shows this exception error. I don't know if there is a problem with the name of regions. Ask for any other information you need.

I hope you could help me, thanks in advance.

has columns:

sample | transcript mean | (all) CDS mean | selection mean | transcript bases < background lower | selection bases < background lower | CDS bases < background lower  | transcript bases < cutoff | CDS bases < cutoff | selection bases < cutoff. 

these values are available from the transcript.stats() function.

where the selection columns are empty when there is no selection.

location.hash should update to, e.g. #gene=KNCQ2&selection={chrom}:{start}-{stop}&depth_cutoff=7

where selection is the hovered/selected region and depth_cutoff is a (to be added) value from the user selected depth cutoff.

currently, a single sample with high coverage makes it impossible to see variation in other samples.

a user can zoom on the y-axis, but we can add a checkbox/toggle that finds the 95th (or 98th) percentile of the data and automatically sets the zoom to that height.

Hi Brent,

Not sure if there's time and/or funding for this, but what would you think about converting this to /adding a MultiQC plugin for this project? (Talking about a real stand-alone plugin, not a module)

Would be nice to be able to include this functionality next to coverage metrics from other sources in a single report.

Thanks
M

This is more apparent when you increase sample size:

Reducing to 10% opacity helps while still preserving an aspect of background:

function highlight_sample(sample) {
    setHashParams({'sample': sample})
    let d = document.getElementById("gene_plot")
    let vals = d.data.map((t, i) => {
        if (t.tracktype == "background") {
            return [1, 1.5]
        }
        if (t.tracktype != 'sample') {
            return [undefined, undefined]
        } else {
            if (t.name == sample) {
                return [1, 2]
            } else {
                return [0.10, 0.36]
            }
        }
    })

    Plotly.restyle(d, {'opacity': vals.map(i => i[0]), 'line.width': vals.map(i => i[1]), 'hovertemplate': vals.map(i => i[1] > 0.8 ? HOVER_TEMPLATE: null)})
}

Open to community suggestions for fixing cases like NEB.

It would be nice to be able to run this on servers with restricted internet access. Would it be possible to have a solution where you could generate a file with transcript info that can be reused in these cases?

# Something like this to generate the file:
seqcover generate-db --genes PIGA,KCNQ2,ARX,DNM1,SLC25A22,CDKL5,GABRA1 \
		--hg19 \
		-o offline_db.json

# Then something like this to use it
seqcover report --genes PIGA,KCNQ2,ARX,DNM1,SLC25A22,CDKL5,GABRA1,CAD,MDH2,SCN1B,CNPY3,CPLX1,NEB,HNRNPA1,CCDC39,AIFM1,CHCHD10 \
		--background seqcover/seqcover_p5.d4 \
		--fasta $fasta samples/*.bed.gz \
		-r my_genes_report.html \
		--offline-db offline_db.json

Nice tool! I have noticed some genes (e.g. HNRNPA1) gives an assertionerror, and I have not been able to figure out why.

code used:

./seqcover report --genes HNRNPA1 \
--fasta $fasta samples/*_recal.per-base.d4 \
--background seqcover_out/seqcover_p5.d4 \
-r my_genes_report.html \
--hg19

# Gives:
fatal.nim(49)            sysFatal
Error: unhandled exception: transcript.nim(143, 14) `r_off - l_off == o_exon[1] - o_exon[0]`  [AssertionError]

Hi,

Not sure I got this right, but... I am using seqcover with the --hg19-flag. Suddenly I get an error with specific genes.

CTDP1 is an example.

./seqcover report --genes CTDP1 --hg19 --fasta ${fasta} -r my_genes_report.html ${d4}
reports the following error:
Error: unhandled exception: d4:error seeking to position: 18:79679792 [ValueError]

I think the problem is that CTDP1 is on the fringe of exon 18, and when I get the coordinates in GRCh38 (for some reason), it has some parts that are outside the hg19-genome.

When I make seqcover print the gene.transcripts object from the get_genes proc, they are identical regardless of the --hg19-flag.

This is more likely something to do with the response from mygene.info, but I wanted to report it here in case somebody else is seeing the same error, or if it is something I am doing wrong.

Some genes return no exons from the query, this gives the following error message.

tables.nim(262)          []
Error: unhandled exception: key not found: exons_hg19 [KeyError]

An example is CCDC39 ("_id": "ENSG00000145075") where the query returns the following results:

# http://mygene.info/v3/gene/ENSG00000145075?fields=name,symbol,exons
{"_id": "ENSG00000145075", "_version": 1, "name": "coiled-coil domain containing 39", "symbol": "CCDC39"}