User: serpalma.v

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serpalma.v20
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Posts by serpalma.v

<prev • 55 results • page 1 of 6 • next >
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Comment: C: bcftool (mpileup, call) extremely slow on 60 BAMs (WGS 20x)
... As I understand it, in order to be cosidered a bed file, the bed extension should be specified: > To indicate that a file be treated as BED rather than the 1-based tab-delimited file, the file must have the ".bed" or ".bed.gz" suffix (case-insensitive). Otherwise, the ``--regions-file`` is trea ...
written 4 days ago by serpalma.v20
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Comment: C: bcftool (mpileup, call) extremely slow on 60 BAMs (WGS 20x)
... I created a test tab delimited file ``regions.txt`` for chr1 and chr2 that looks as follows: 1 1 195471971 2 1 182113224 Column 1 corresponds to CHROM, column2 to POS and column3 to POS_TO. According to the corresponding documentation: > The columns of the tab-delimited fil ...
written 4 days ago by serpalma.v20
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bcftool (mpileup, call) extremely slow on 60 BAMs (WGS 20x)
... I am trying to run bcftools (v1.9) mpileup on 60 BAM files from WGS (~20x). bcftools mpileup -Ou -f ref.fa $(echo $BAM_LIST) | bcftools call -vmO z -o out.vcf.gz The job started 20 days ago. The out.vcf.gz shows that it has gone through 10 chr (~2ds/chr). There are still 9 autosomes, 2 sex ch ...
bcftools samtools mpileup snp wgs written 5 days ago by serpalma.v20
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Comment: C: GATK variantFiltration unexpected behaviour?
... I've encountered the same issue. Could you please provide your solution if you were able to fix this problem? ...
written 20 days ago by serpalma.v20
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Comment: C: Only females but still few reads map to Y chromosome
... Ok this is a relief... From what I gather so far, this is an issue that requires further examination rather than elimination. Would you agree? ...
written 4 weeks ago by serpalma.v20
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Comment: C: Only females but still few reads map to Y chromosome
... Could you please elaborate on what you mean with "distinct areas"? ...
written 4 weeks ago by serpalma.v20
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Comment: C: Only females but still few reads map to Y chromosome
... I am using Mus_musculus.GRCm38.dna.primary_assembly from ensembl ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz ...
written 4 weeks ago by serpalma.v20
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Only females but still few reads map to Y chromosome
... Hello! I have been provided a data set (WGS) consisting of only female mice. After finishing the alignments with bwa I ran picard's BAMIndexStats. Surprisingly, the Y chromosome had reads mapped to it [Fig1][1], but they were very few compared to the rest of the reference genome [Fig2][2]. I wou ...
wgs alignment bwa written 4 weeks ago by serpalma.v20 • updated 4 weeks ago by Pierre Lindenbaum115k
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Comment: C: Per base GC content with a shoulder after adapter removal and trimming
... The sample was already processed with trimmomatic, including adapter removal. FastQC did not detect adapters. The quality Phred score was above 28 for all bases. ...
written 10 weeks ago by serpalma.v20
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Comment: C: Per base GC content with a shoulder after adapter removal and trimming
... I added that to the post. It is WGS data ...
written 10 weeks ago by serpalma.v20

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