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@Sveta:
just in case you haven't noticed: your funtion 'read_value' only works for the first chromosome. You need to add up the lengths of the preceding chromosomes.
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sorry to bother you,when i use this tool,it got the following error
could you please help me out
(py3) ➜ SCCNV git:(master) ✗ python sccnv_v1.0.py -i ./tmp/bamlist.txt -o ./tmp/cellAtoC -k Tr…
Lav-i updated
1 month ago
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Hi,
I'm attempting to run sequenceTools to generate pseudo-haploid calls for a list of bamfiles.
However I'm getting the following error:
pileupCaller: SeqFormatException "cannot parse chromos…
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This happens a lot during genome loading:
```
INFO:root:Loading genome from genbank file (7 of 150) AM946981.gb
WARNING:root:Duplicate genes B21_02159 on chromosome 8943870
WARNING:root:Duplicate gen…
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Hello!
I am scanning the human genome for CTCF motifs using a PWM-format matrix:
```console
moods-dna.py --sep ";" -s hg38.fna --p-value 0.0001 -S MA0139.1_pwm -o ctcf_scan
```
File hg38.fna co…
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Suggestion from Ryan because he did not find it obvious that clicking on the chromosome again once expanded takes you back to all
![screen shot 2018-07-31 at 15 38 11](https://user-images.githubuse…
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Looking only at chromosome 3, some 2k rsIDs (from 23andMe data) are not found in the 2.8G SNPs in imputed chromosome 3... Why should SNPs be dropped from the input in the output?
Many thanks.
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Hi Brent,
Thanks for a really great tool. it's blazing fast!
I'm testing vcfanno to add GnomAD annotations for some WGS data. There's one GnomAD WGS VCs per-chromosome, so I have 23 separate [[ann…
drmjc updated
6 months ago
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Dear Xingtan,
When I use partition_gmap.py to separate chromosome group for fasta and BAM, some chromosomes didn't have any bam file but fasta file.
Do you have any ideas for it or anyway to chec…
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In the following example of structural variants, ideally, we can remove chromosomes that do not contain any events (e.g., `chr1`).
We could support this by using custom assembly specification:
…