User: ja4123

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ja41230
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Posts by ja4123

<prev • 18 results • page 1 of 2 • next >
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How to convert vcf.bgz to vcf.gz?
... I am looking for some quick way to convert vcf.bgz to vcf.gz, any advise? Thanks in advance for the help. ...
vcf bgz gz gnomad written 10 days ago by ja41230 • updated 10 days ago by Pierre Lindenbaum125k
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How to read vcf file in python?
... When I try to do simply like this: import vcf vcf_reader = vcf.Reader(filename="in.vcf.gz") there is an error: AttributeError: partially initialized module 'vcf' has no attribute 'Reader' (most likely due to a circular import) But vcf module has that attribute .. Kindly help. ...
vcf python reader written 10 days ago by ja41230 • updated 4 days ago by metageni100
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Comment: C: Problem succesfully running freebayes
... Okey, so any advise which file has to bo modified and which way? ...
written 11 days ago by ja41230
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Comment: C: Problem succesfully running freebayes
... gunzip -c in.vcf.gz | grep -v '# ' | cut -f 1 | uniq output are metadata from vcf and column #CHROM, that is: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY chr1_KI270706v1_random chr4_GL000008v2_random chr7_K ...
written 11 days ago by ja41230
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Comment: C: Problem succesfully running freebayes
... Something like that: chr1 chr10 chr11 chr11_KI270721v1_random chr12 chr13 chr14 chr14_GL000009v2_random chr14_GL000225v1_random chr14_KI270722v1_random and so on. Numbers from 1 to 64185939 - in second case ...
written 11 days ago by ja41230
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Problem succesfully running freebayes
... 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 Before change headers in fasta from chr1, chr2 .. to 1, 2, 3 ... , I had error: unable to find FASTA index entry for '1' Now, after ch ...
vcf fasta freebayes written 11 days ago by ja41230
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File not suitable for fasta index generation.
... 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 And I had error like this: unable to find FASTA index entry for '1' I have changed the headers in fasta file from chr1, chr2 ... to 1, ...
fasta freebayes index written 11 days ago by ja41230 • updated 11 days ago by Pierre Lindenbaum125k
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Comment: C: HISAT2 Error: Encountered internal HISAT2 exception (#1)
... Output of youre command: Command 'hisat2' not found After mine change: hisat2-align-s --dta -x name_tran -1 input1.fastq.gz -2 input2.fastq.gz -S out.sam I get the same error: Error: reads file does not look like a FASTQ file Memory is about 80 GB ...
written 20 days ago by ja41230
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Comment: C: HISAT2 Error: Encountered internal HISAT2 exception (#1)
... input1.fastq.gz: gzip compressed data, was "input1.fastq", last modified: Fri Jan 3 10:46:39 2020, from Unix input2.fastq.gz: gzip compressed data, was "input2.fastq", last modified: Fri Jan 3 10:45:58 2020, from Unix ...
written 20 days ago by ja41230
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Comment: C: HISAT2 Error: Encountered internal HISAT2 exception (#1)
... You know, I have change the command: hisat2-align-s -p 8 --dta -x name_tran -1 input1.fastq.gz -2 input2.fastq.gz -S out.sam And now I have error like this: Error: reads file does not look like a FASTQ file terminate called after throwing an instance of 'int' Aborted (core dumped) ...
written 20 days ago by ja41230

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