User: bwczech

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bwczech0
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Posts by bwczech

<prev • 31 results • page 1 of 4 • next >
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Comment: C: How to split BAM files by samples from PacBio
... Ok, Thank you, Now I understand. I used that parameters for lima, but I do not understand sth. I used 3 barcodes for 1 run (on 1 rune we have 3 samples sequenced), but lima produced 6 bams – every combination of my barcodes (025 forward with 025 forward; 025 forward with 0032 forward; 0032 forward w ...
written 4 days ago by bwczech0
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Comment: C: How to split BAM files by samples from PacBio
... Yes, I tried with that function and lima created about 900 bam files (with barcode prefix) and I do not know how can I identified my samples (because of plenty BAM files). ...
written 6 days ago by bwczech0
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Comment: C: How to split BAM files by samples from PacBio
... Yes. In my fasta with barcodes there are about 300 barcodes... ...
written 6 days ago by bwczech0
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How to split BAM files by samples from PacBio
... Hi, I have sequences from 6 bacterias (E. Coli and Salmonella). 6 samples have been sequenced using PacBio on 4 movies so I have 3 bax files for every movie (12 in total). I converted bax file to bam using Bax2Bam and then I used Lima to do demultplexing (using a set of about 330 barcodes in fasta ...
bax bam pacbio written 7 days ago by bwczech0 • updated 5 days ago by jharting0
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Summary statistics of VCF annotated files (snpEff)
... Hi, I have 30 annotated VCF files (for each chromosome) in snpEff. I would like to do summary statistics and compare number of differents effect between chromosomes (or between autosomes and sex chromosomes). I have extracted ANN field from my VCF file (using short BASH script). And it is looks lik ...
vcf annotation snpeff statistics written 8 days ago by bwczech0
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Comment: C: snpEff assigned all variants as modifier intergenic
... I see the problem is during building a database... Look here: Reading sequence '1', length: 158534110 Adding genomic sequences to exons: Done (1857 sequences added, 0 ignored). Reading sequence '2', length: 136231102 Adding genomic sequences to exons: Done (0 sequences added, 0 i ...
written 23 days ago by bwczech0 • updated 1 day ago by finswimmer7.0k
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Comment: C: snpEff assigned all variants as modifier intergenic
... Now I compared all files. The 1st chromosome is annotated fine, but other are not. In 1st chromosome I have many types of snp localisations, but in other all snps are intergenic... ...
written 23 days ago by bwczech0
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snpEff assigned all variants as modifier intergenic
... Hi! I have following problem: I have used a snpEff for annotation my VCF files. I created database (I have a custom gff and reference genome). Every time snpEff detect all my snps as a intergenic (modifier). It is not true. Sth is wrong, but I do not know what. Can you help me? Any suggestions? ...
vcf ngs snpeff written 24 days ago by bwczech0
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Psuedoautosomal regions in reference genome
... Hi, I have reference genome (ARS-UCD1.2_Btau5.0.1Y). How can I check if that genome contain pseudoautosomal region on both chromosomes and also how can I find that regions in gff file? How can I check also, how many reads have been aligned to pseudoautosomal regions. thank you ...
reference genome par written 4 months ago by bwczech0
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Comment: C: Ambiguous position in SNPdb file and reference genome
... SNPdb file is ARS1.2PlusY_BQSR.vcf.gz, reference genome is ARS-UCD1.2_Btau5.0.1Y.fa ...
written 4 months ago by bwczech0

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Popular Question 4 months ago, created a question with more than 1,000 views. For Cluster analysis for SNPs data in R
Popular Question 4 months ago, created a question with more than 1,000 views. For Comparing two columns and replace in R Package

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