User: screadore

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screadore0
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Posts by screadore

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Does anyone know any ANNOVAR alternatives for Whole Genome Sequencing with flexible filters for annotations of a VCF file?
... Hello everyone, I'm looking to find alternatives to ANNOVAR whole genome sequencing annotations that offers flexible filtering options for non-coding regions of DNA? If anyone has any experience of open source tools used for this please let me know. Thank you. ...
genome annotations sequencing written 22 hours ago by screadore0
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Having trouble running ANNOVAR annotator for the first time please help!
... Hey guys so I'm trying to run ANNOVAR for the first time on a Windows x64 Dell laptop. The following issues have occured: H:\>perl C:\Users\SCreadore\Desktop\annovar\table_annovar.pl example/ex1.avinput humandb/ -buildver hg19 -out myanno -remove -protocol refGene,cytoBand,dbnsfp30a -operati ...
software error written 7 days ago by screadore0
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Comment: C: Need help changing RNA-seq code from histat aligner into Star aligner please.
... I honestly don't know it's one of my colleagues issue and I'm just trying to help her figure it out. ...
written 13 days ago by screadore0
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Comment: C: Need help changing RNA-seq code from histat aligner into Star aligner please.
... The only issue is for the lab we need to use the pipeline provided above. ...
written 13 days ago by screadore0
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Comment: C: Need help changing RNA-seq code from histat aligner into Star aligner please.
... Thank you very much for the reply. Could you give me some insight into how to go about replacing the hisat2 with STAR in the sample script file? I'd greatly appreciate it. Thank you again. ...
written 13 days ago by screadore0
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Need help changing RNA-seq code from histat aligner into Star aligner please.
... I need help converting histat aligner into star aligner for this script. Please let me know what I could do. Link to the full code is here: https://github.com/JustinGibbons/USF_Omics_Hub/blob/master/RNA-Seq_Pipeline/rna_seq_pipeline.py def write_out_hisat_array_slurm_file(arguments_file,outfile ...
rna-seq written 13 days ago by screadore0

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