User: storm1907

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storm19070
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Posts by storm1907

<prev • 42 results • page 1 of 5 • next >
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tissue specific gene list
... 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! ...
rna-seq written 15 days ago by storm19070 • updated 15 days ago by Fabio Marroni2.6k
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whole exome variant filtering
... 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! ...
next-gen written 20 days ago by storm19070
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Variant calling with duplicates
... 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! ...
next-gen written 4 weeks ago by storm19070
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convenient VCF comparison
... 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 ...
sequencing written 7 weeks ago by storm19070
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Comparing CoV2 sequences
... 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 ...
sequence written 9 weeks ago by storm19070
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rename files in a directory
... 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! ...
unix written 11 weeks ago by storm19070 • updated 11 weeks ago by Joe18k
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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 storm19070
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FASTA file header
... 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 ...
consensus written 11 weeks ago by storm19070
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LoFreq input file issues
... 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 ...
assembly written 11 weeks ago by storm19070
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Comment: C: correct header with samtools mpileup
... 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 storm19070

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