User: storm1907
storm1907 • 0
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Posts by storm1907
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... Hello,
I would like to download all expressed gene list for only one tissue type (testis) from GTEX. I am bit confused, what table should I pick (found plenty of datasets in https://gtexportal.org/home/datasets), and what are these gct files.
Thank you for a help!
...
written 15 days ago by
storm1907 • 0
• updated
15 days ago by
Fabio Marroni • 2.6k
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... Hello,
I need to do whole exome variant analysis from ready vcf.gz files. Only option I know is filtering through Illumina Variant Interpreter
Are there better options for whole exome variant filtering than Variant Interpreter?
Thank you! ...
written 20 days ago by
storm1907 • 0
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... Hello,
I would like to check how viral RNA Seq called variants look before read duplicate removal.
However, when I try to filter seq files with duplicates, I only have empty output
Are variant callers supposed to work with duplicates?
Thank you! ...
written 4 weeks ago by
storm1907 • 0
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... Hello,
can anybody suggest a good tool for vcf comparison of LoFreq vcfs and other kind of vcfs
I tried VCFToolZ , but it is not suitable for LoFreq outputs and does not draw Vienn diagrams
Also BCFTools isec and stat output is plenty of txt files, and it takes time to summarize them altogether
But ...
written 7 weeks ago by
storm1907 • 0
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... Hello,
I am in need to find the countries that have most similar CoV2 sequences with my country - to download a list of sequences and/or country names.
I did not find such an option on GISAID. Is that somehow possible? Or it is possible on NEXTSTRAIN? I could find only region visualisation in there
...
written 9 weeks ago by
storm1907 • 0
1
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... Hello,
I need to move vcf file extensions in a directory from upper to lower case
I have files ABC.VCF, but I need them to ABC. vcf
what would be correct comand line in UNIX?
Thank you! ...
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Comment:
C: FASTA file header
... It takes sample name from the vcf file
> sample_name
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
...
written 11 weeks ago by
storm1907 • 0
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... Hello,
I am trying to convert my vcf files to fasta. However, after aligning to reference, vcf ID from the header disappears, and bcftools/vcftools are writing only reference seq name in file header.
Like > NC_xxxx.1
Any ideas?
I run consensus script like
for file in $inpath/*.vcf ;
d ...
written 11 weeks ago by
storm1907 • 0
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... Hello,
when trying to run Lofreq tool for low frequency variant calling with mpileup files, the tool is looking for header in the input (but there should not be one)
when running Lofreq with binary files, tool does not work either
Here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526318/ it is sai ...
written 11 weeks ago by
storm1907 • 0
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... So I should not expect any header? OK, will try to check out, why my downstream tool is asking for it
Thanks! ...
written 11 weeks ago by
storm1907 • 0
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