User: ja4123

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ja41230
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Posts by ja4123

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Comment: C: HISAT2 Error: Encountered internal HISAT2 exception (#1)
... I am useing this procedure: Align the RNA-seq reads to the genome Map the reads for each sample to the reference genome: $ hisat2 -p 8 --dta -x chrX_data/indexes/chrX_tran -1 chrX_data/samples/ERR188044_chrX_1.fastq.gz -2 chrX_data/samples/ERR188044_chrX_2.fastq.gz -S ERR18804 ...
written 6 weeks ago by ja41230
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HISAT2 Error: Encountered internal HISAT2 exception (#1)
... Hello, I am using HISAT2 for aligning transcripts to the reference genome. I have build the indexes first. And try the command as follows: hisat2-build -p 8 --dta -x name_tran -1 input1.fastq.gz -2 input2.fastq.gz -S out.sam However, I am getting the following error: Error: Encountered in ...
hisat2 written 6 weeks ago by ja41230
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Comment: C: Unable to find FASTA index entry for '1'
... There is some quick way to change prefix in one of that two files? ...
written 9 weeks ago by ja41230
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Unable to find FASTA index entry for '1'
... Hey, I have a sorted and indexed .bam file, and I am running it through freebayes, with the script : freebayes -f ref.fa -@ in.vcf.gz aln.bam >var.vcf very time I run this script I get the: unable to find FASTA index entry for '1' Even know I have the index files. I have the correct ...
fasta vcf bam freebayes written 9 weeks ago by ja41230
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How to read vcf.bgz or vcf.gz in python using PyVcf?
... When I try to do simply like this: vcf_reader = vcf.Reader(open("input.vcf.gz", 'r')) vcf_writer = vcf.Writer(open('input.vcf.gz', 'w'), vcf_reader) there is an error: UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte ...
vcf python pyvcf written 9 weeks ago by ja41230 • updated 9 weeks ago by dariober11k
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Comment: C: VCF filtering by depth
... How to filter AF in vcf file with that way? There is a KeyError. ...
written 10 weeks ago by ja41230
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Require Genotypes In Vcf File In Order To Output Frequency Statistics
... I have a merged .vcf file, that although wasn't merged using vcftools seems almost identical to vcf-merge files. If I try and use --freq to calculate allele frequencies from this file I get the error message "Require Genotypes in VCF file in order to output Frequency Statistics". This seems odd as t ...
vcf allele frequency vcftools af written 10 weeks ago by ja41230
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How to load bed graph in a numpy vector
... Someone can tell me how to load bed graph format to numpy as a vector? Part of a file looks like that: 4 13636 13687 1 4 13748 13799 1 4 26733 26754 1 4 26754 26776 2 4 26776 26785 3 4 26785 26791 4 ...
gene sequence written 9 months ago by ja41230 • updated 9 months ago by WouterDeCoster42k

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