chanjo

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Adds calculate mean coverage for genes in samples. Adress #190

1

moonso

Chanjo version 4.2.0 installed via pip. This is the log. ``` chanjo init -a -f 2018-08-31 11:38:49 cybertron chanjo.init.cli[10816] INFO setting up chanjo under: /data/coverage180830 2018-08-31 11:38:49 cybertron chanjo.init.bootstrap[10816] INFO...

biocyberman

It should be possible to detect when chrom X coverage is more than expected for a "male" sample. Usually a male has lower X coverage than a female.

robinandeer

calculate gene / interval is missing

2

Hi I can see that earlier versions of change the change calculate contained both gene and interval as subcommands, however in the recent version only contains "mean" as the only...

mjlarsen

chanjo generates errors instead of help text

6

``` $chanjo Traceback (most recent call last): File "/mnt/hds/proj/cust003/develop/modules/miniconda2/envs/mip4.1/bin/chanjo", line 11, in load_entry_point('chanjo==4.0.0', 'console_scripts', 'chanjo')() File "/mnt/hds/proj/cust003/develop/modules/miniconda2/envs/mip4.1/lib/python2.7/site-packages/click/core.py", line 716, in __call__ return self.main(*args, **kwargs) File "/mnt/hds/proj/cust003/develop/modules/miniconda2/envs/mip4.1/lib/python2.7/site-packages/click/core.py", line 695, in main...

henrikstranneheim

I have many overlap amplicons. Through the bam file , I can get the pair reads start and end . The pair reads' start and end is completely match to...

tiehan

Perhaps it's possible to write the test to also report when there's ambiguity in the sex determination For example when there's some reads on X but not enough to call...

robinandeer

Wrong strand info in the ccds.15.grch37p13.extended.bed?

3

I don't know why the `strand` values for all exons are `-` minus. ``` coverage ➤gawk '{print $6}' ccds.15.grch37p13.extended.bed |sort|uniq - ```

biocyberman

Use GTF/GFF instead of CCDS bed?

2

I have been detached from work that uses `chanjo` for a while I get outdated when I come back now. It is indeed a good think to see how `chanjo`...

biocyberman

joined gene names, a possible pitfall to cause incorrect result?

2

Is `chanjo` aware of this problematic gene names, which may causes various problems for queries that base on gene names? ``` bash ➤ gawk '{print $NF}' ccds.15.grch37p13.extended.bed|grep ','|head NOX1,NOX1,NOX1 NOX1,NOX1,NOX1...

biocyberman