User: agathejouet

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Posts by agathejouet

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Comment: C: bcftools merge, error "Could not parse the region(s)"
... Thanks very much for your help, will try to modify this! Agathe ...
written 6 weeks ago by agathejouet0
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Comment: C: bcftools merge, error "Could not parse the region(s)"
... The output is: LOC_Os01g16370_chr1:9292171..9298764_UTR-0 LOC_Os01g16400_chr1:9313135..9317036_UTR-0 LOC_Os01g21240_chr1:11854526..11857948_UTR-0 LOC_Os01g25630_chr1:14525576..14530578_UTR-0 LOC_Os01g25710_chr1:14570811..14580124_UTR-0 LOC_Os01g25810_chr1:14611521..14616096_ ...
written 6 weeks ago by agathejouet0
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bcftools merge, error "Could not parse the region(s)"
... Hi all, I am trying to merge multiple vcf files using bcftools version 1.6. Unfortunately, I receive the following error for all of my "chromosomes": [E::_regions_init_string] Could not parse the region(s): chr1 ex: [E::_regions_init_string] Could not parse the region(s): JA218_chr6:299 ...
vcf merge bcftools tabix written 6 weeks ago by agathejouet0 • updated 6 weeks ago by Pierre Lindenbaum101k
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Answer: A: Pipeline design: from reads to consensus sequences of multiple individuals
... Hi all, In the end, I decided to extract annotated genes from the reference fasta to produce a new fasta and align the reads to those. Not what I really wanted but good enough... Agathe ...
written 10 weeks ago by agathejouet0
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Comment: C: Pipeline design: from reads to consensus sequences of multiple individuals
... Bedtools intersect removes reads aligned outside of my genes but keep the scaffolds as they are in my bam, which is not what I want... Will keep looking. ...
written 10 weeks ago by agathejouet0
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Comment: C: Pipeline design: from reads to consensus sequences of multiple individuals
... Thanks for your answer Kevin. It is indeed whole-genome sequencing although sequencing was done a while ago, with short reads (86 bp PE). That is why I would prefer a pipeline based on mapping instead of assembly. I am not sure what you mean with the second option, merging all reads together. How ...
written 10 weeks ago by agathejouet0
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Pipeline design: from reads to consensus sequences of multiple individuals
... Hi all, I am having an issue with a pipeline design. I have a reference genome in fasta format as well as a gff file containing the position of annotated genes in that genome. I also have reads from several individuals of the reference genome species. My aim is to get the consensus sequence of all ...
consensus pipeline alignment variant mapping written 11 weeks ago by agathejouet0
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Comment: A: Why is bwa terminating alignment and exiting the script without an error message
... Hi, I am having the same problem here. Anyone with a clue of what is happening? I am using the following command: source bwa-0.7.15; source samtools-1.3.1; bwa mem -t 4 ref_fasta read1 read2 | samtools view -hbS - | samtools sort - -o outbam.sorted It has worked fine for al ...
written 5 months ago by agathejouet0

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