Songtao Gui

Failed to display bam alignment details if the CIGAR has "H" or "S"

4

Hi, @lidaof I was trying to display bam file using WashU browser v48.5.3, however, some of my bam records could not be correctly parsed: > The cigar of this alignment...

How to build my own snp search database and add a snp track to browser?

3

Hi, @lidaof I have some local snp.vcf files, and would like to build a snp search function as http://epigenomegateway.wustl.edu/browser/ does. Is there a detail manual for that? And I have...

exa automatically expands softlinks when embedded in a pipe

2

Hi, I found that exa would automatically expands softlinks when embedded in a pipe (I am using exa `v0.9.0` on linux `CentOS7`): ```sh > ls | cat raw_AAA.txt raw_AAB.txt sl_AAA.txt...

How to setup h5ai to be accessible through sub URL paths?

1

Hi, I was trying to build a h5ai server within a sub URL path like "www.xxx.com/mysite/ftp", but I failed to make h5ai accessible through URLs of "/subpath/h5ai" format. So I...

'Analysis' sidebar option in gene detail page in Tripal3

9

Hi, In tripal2 there is an 'Analysis' sidebar option in the gene detail page: > which shows analysis related to this gene feature:  However, in tripal3, this sidebar was...

added "*" in ALT after genotyping

1

Hi, After running `BayesTyper genotype`, the output vcf file added `*` allele to the `ALT` field. For example: This is the input record, the `ALT` field only contains `T` allele...

Got problem when trying to liftover bam file

3

Hi, I would like to liftover some bam files. But I got some errors when testing: ```shell # input cmd CrossMap.py bam test.chain test.bam # logs and errors Insert size...

Control the empty lines in the usage doc

2

The generated Usage contains many empty lines, I understand this may help for better layout when the usages are short. However, when the options gets complicated, the whole usage doc...

type 'exceptions.IOError': Broken pipe

2

Hi, I'm running metaSV with cmd like: `run_metasv.py --reference /home/gst/work/ref/Zea_mays.AGPv4.dna.toplevel.fa --boost_sc --pindel_vcf Q417_pindel.vcf --breakdancer_vcf Q417_breakdancer.vcf --cnvnator_native Q417_cnvnator.out --manta_vcf Q417_manta.vcf --lumpy_vcf Q417_lumpy.vcf --wham_vcf Q417_whamg.vcf --mean_read_length 150 --sample Q417 --bam /home/gst/work/b73_BWAMEM_bam/Q417_bwa/Q417.bwamem.sort.bam --spades...

Hi, I have tested my sequenceTubeMap server with the build in test data `xy-test`, and everything works fine. However, when come up with my own data, the server failed to...