dodofly

如果想在表格内显示 | ，无法完成。因为 | 会被认为是表格格式，转义 \| 无效果，在别的一些markdown 工具可以。

Dose bulk-RNA data batch matter?

1

If my bulk-RNA-seq data obtain from different time, does this matter?

delly2 outputs duplicate results?

1

Hello, delly2 is giving me duplicate results like: ```bash chr20 30422589 INV00028117 C 429 PASS PRECISE;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.9.1;END=56101675;PE=4;MAPQ=60;CT=3to3;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=57;INSLEN chr20 30422589 INV00028117 C 429 PASS PRECISE;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.9.1;END=56101675;PE=4;MAPQ=60;CT=3to3;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=57;INSLEN chr20 30422589 INV00028117 C 429 PASS PRECISE;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.9.1;END=56101675;PE=4;MAPQ=60;CT=3to3;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=57;INSLEN...

*_genes.out duplicate genes

3

Hello, thanks for your good tool! My problem is some genes are duplicated in *_genes.out result. I used hisat2 to align reads. ```bash TPMCalculator -g ${GRCh38GTF} -b ${BamDir}/${Sample}.bam \ -c...

GRCh38 blacklist contains overlap in bed file

2

For example ``` chr16 34586660 34587100 chr16 34587060 34587660 chr20 31067930 31069060 chr20 31069000 31069280 ``` This will cause same tools error, for example `bamCoverage` of deeptools.

DOWNLOAD_DELAY will not work if use proxy.

1

Hello, It seems scrapy spider's `DOWNLOAD_DELAY` will not work if I use this proxy. In my script I set `DOWNLOAD_DELAY=8` and enable random `DOWNLOAD_DELAY`。 ``` custom_settings = { "RETRY_TIMES": 7,...

Need help with error: no VCF_dict_tmp

2

Hi, I used install.sh to installed this sofeware, how ever when I test it by using test file of this software, it seems missing file/dir VCF-dict_tmp. I think there may...

Add version information for dependencies?

2

Hello, the file `env.yml` specifies dependencies for this project. But I think it will be better to specify their versions together because conda/pip will install the newest package by default...