User: Chvatil

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Chvatil50
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Posts by Chvatil

<prev • 146 results • page 1 of 15 • next >
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Dowload Structural variant VCF file from 1000genome website
... Hello everyone, I have just mapped reads from a human genome: **HG00157** against the reference genome : **GRCh38** Do you know where I can find the corresponding VCF structural variant file? (a priori it is phase 3 but it seems that on the site of the 1000 genomes it only corresponds to the varian ...
genome assembly mapping variants written 8 days ago by Chvatil50
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Extract specific variant genome ID from a VCF file
... Hello I have a specific variant file (vcf) dowload from ftp:/­/­ftp.­1000genomes.­ebi.­ac.­uk/­vol1/­ftp/­data_collections/­1000_genomes_project/­release/­20190312_biallelic_SNV_and_INDEL/­ALL.­chr9.­shapeit2_integrated_snvindels_v2a_27022019.­GRCh38.­phased.­vcf.­gz.­tbi so I get a file ca ...
genome vcf variant written 9 days ago by Chvatil50 • updated 9 days ago by Jorge Amigo12k
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Comment: C: Difference between mate-pair, paired-end and long read
... Thank you for this explanation, so If I'm not wrong we can use long read and mate pair in order to assemble contigs together (scaffolding) right ? I'm asking this question because wen I have assemblies made only from short paired-end, I have incorrect assembly where I see `misassembly breakpoints` a ...
written 13 days ago by Chvatil50
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Comment: C: Difference between mate-pair, paired-end and long read
... Oh sorry I did not know that, someone gave me an answer then I cannot delete it now.. ...
written 14 days ago by Chvatil50
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Difference between mate-pair, paired-end and long read
... Hello everyone, I writing here because I have some questions for you. I wondered what the essential differences were between `paired-end`, `mate-pair` and `long read`? for me `mate-pair` and classic `paired-end` are both `paired-end reads`, with the difference that : 1. For classical `paired-e ...
assembly read written 14 days ago by Chvatil50
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retrieve the properties of the reads on NCBI on the command line
... Hi everyone, I was wondering if anyone knows a quick way by command line to find information on the reads used for an assembly, by information I mean especially if it was `paired end` or `mate end` since if it is only an assembly made by pairend I will use **Reapr** in order to break missasemblies s ...
reads assembly ncbi written 15 days ago by Chvatil50
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Comment: C: HISAT2- (ERR): hisat2-align exited with value 134
... OK I found the issue, it came from the fact that some fastq.gz files had .1 extension after the .gz. ...
written 5 weeks ago by Chvatil50
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Comment: C: HISAT2- (ERR): hisat2-align exited with value 134
... Well I changed it and got the following message now ... Saw ASCII character 35 but expected 64-based Phred qual. Try not specifying --solexa1.3-quals/--phred64-quals. terminate called after throwing an instance of 'int' Aborted (ERR): hisat2-align exited with value 134 ...
written 5 weeks ago by Chvatil50
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Comment: C: HISAT2- (ERR): hisat2-align exited with value 134
... Thank you I will try that ...
written 5 weeks ago by Chvatil50
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detect and correct misassemblies in eucaryotic scaffolds
... Hello everyone, I actually made several assembly of eukaryotic genomes and I found some missasemblies in the file by mapping reads against the fasta assembly file. So I wondered if someone knew a performant tool in order to `identify` an `correct misassemblies` in scaffolds for `eucaryotic genomes` ...
mec reapr assembly written 5 weeks ago by Chvatil50

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