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Tag: bioinformatics

Lifting over GWAS summary statististic file from build 38 to build 37

I am using the UCSC lift over tool and the associated chain to lift over the results of my GWAS summary statistic file (a tab separated file) from build 38 to build 37. The GWAS summary stat file looks like: Follwing is the UCSC tool with the associated chain I am using: liftover: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftOver chain file: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz I want to

How to make the bash script work with one command after another?

I have a bash script like below. First it will take sorted.bam files as input and use “stringtie” tool give each sample gtf as output. Then path for each sample gtf will be given into mergelist.txt. and then use “stringtie merge” on them to get “stringtie_merged.gtf”. I totally have 40 sorted.bam files. I separated the commands with ; After running

blast could not create a unit counts container

I build a blast local database. However, when I run the blastn command I got this error message: T0 “/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_250088_130.14.22.10_9008__PrepareRelease_Linux64-Centos_1448906370/c++/compilers/unix/../../src/algo/winmask/seq_masker_istat_factory.cpp”, line 170: Error: ncbi::CSeqMaskerIstatFactory::DiscoverStatType() – could not open T0 “/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_250088_130.14.22.10_9008__PrepareRelease_Linux64-Centos_1448906370/c++/compilers/unix/../../src/algo/winmask/seq_masker_istat_factory.cpp”, line 271: Error: ncbi::CSeqMaskerIstatFactory::create() – could not create a unit counts container I am using this command to create the blast local database: And this is my command for executing

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