User: bwczech

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bwczech0
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Posts by bwczech

<prev • 23 results • page 1 of 3 • next >
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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 weeks 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 weeks ago by bwczech0
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Ambiguous position in SNPdb file and reference genome
... Hi, I have problem with ambiguous base in SNPdb (BQSR) file and reference genome. The first 2 line of SNPdb (BQSR) looks like: CHROM POS ID REF ALT QUAL FILTER INFO 1 162362 rs477108567 G A . . . so that seems in position 162362 in 1 chromosome in my reference genome I should expect ...
ngs reference snp written 4 weeks ago by bwczech0 • updated 4 weeks ago by Pierre Lindenbaum111k
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Annotation to Btau_5.0.1
... Hi, Could you tell me when can I find an annotation file to Btau_5.0.1 genome. In Ensembl database, only annotation for older version and to UMD3.1 are available. Thank you in advance. ...
genome annotation cattle written 5 weeks ago by bwczech0 • updated 5 weeks ago by h.mon18k
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Read group information
... Hi, I have aligned my files from many lines and I forgot to put information about a Read Group (RG). I know, that Picard MergeSamFiles is requiring that information in bam files. I have used a BWA software for alignment and I didn't use a -R option. I have found a program called AddOrReplaceReadG ...
gatk picard read group bwa written 6 weeks ago by bwczech0 • updated 6 weeks ago by WouterDeCoster31k
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Comment: C: Per tail sequence quality fail
... I have presented graph after trimming (using trimmomatic). Does it means, that aligner (such as BWA) can handle with this tiles problem? ...
written 10 weeks ago by bwczech0
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Comment: C: Per tail sequence quality fail
... Ok. Thank you so much! So program for alignment can handle with it? I thought that I need to do TILE FILTERING using FilterByTile.sh software. So that step is unnecessary? I can normally do alignment with this tiles problem? ...
written 10 weeks ago by bwczech0
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Per tail sequence quality fail
... Hi again! I have another problem with my data. FastQC returns red flag in per tile sequence quality. I see that this problem is often associated with reverse read of sequencing (in few lines). That data are representing WGS. In other files I see horizontal red line through one tile. What can I d ...
quality tile fastqc written 10 weeks ago by bwczech0 • updated 10 weeks ago by Devon Ryan82k
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Per base sequence quality and per base N content
... Hi, I have one incomprehensibleness with my FastQC's report. Usually N's have quality=2, so if our N content in e.g 99bp = 35% we should observe these on the first plot. I attached printscreens from my FastQC and I have a question: if on 99bp N's content >30%, and quality of N =2, why I cannot ...
quality fastqc written 12 weeks ago by bwczech0
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Integrated DNA and RNA sequences in expression analysis
... Hi, How to integrate a dna (WGS) and rna (RNA-seq) in genes expression analysis. I have three individuals with their whole-genome sequences (3 samples) and moreover I would like to get their transcriptome sequences from their 2 tissues (2 x 3 samples). How to use DNA and RNA together to analysis ...
dna-seq rna-seq written 8 months ago by bwczech0 • updated 8 months ago by ori50

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