User: marina-orlova

gravatar for marina-orlova
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Russian Federation
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8 months, 2 weeks ago
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4 years, 11 months ago
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Posts by marina-orlova

<prev • 55 results • page 1 of 6 • next >
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Comment: C: Polymerase slippage filtering
... the platform was illumina ...
written 8 months ago by marina-orlova70
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Polymerase slippage filtering
... Hi! Is there any tools to filter out false positive variants due to polymerase slippage? (AAAAAAinsA for example) Or any callers which perform such filtering. I have total-rna, and abnormally high percent of mutations (about of 30%) are indels in homopolymers. Maybe a bad polymerase..I don't know. ...
rna-seq variants written 8 months ago by marina-orlova70 • updated 4 months ago by Biostar ♦♦ 20
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Sanger dye blobs correction
... Hi Is there any tool which can recognize and replace dye blobs with N in Sanger ABI files? I haven't worked with Sanger reads yet, maybe it is not such a problem not to do anything with them, will it make problems while mapping?   ...
sanger quality-control dye-blobs written 3.5 years ago by marina-orlova70
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Comment: C: Short Tandem Repeats analysis
... thank you for the answer! ...
written 3.5 years ago by marina-orlova70
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Comment: C: Short Tandem Repeats analysis
... Yes, NGS data. hg19 is a reference genome ...
written 3.5 years ago by marina-orlova70
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Short Tandem Repeats analysis
... I need to analyze 3 nucleotides tandem repeats, which tool is best in your opinion for this goal? I looked for this on Biostars but the last answer I managed to find was 2.5years ago. People told about lobSTR and NTRFinder. Are there any new good tools?   ...
tandem-repeats written 3.5 years ago by marina-orlova70 • updated 3.5 years ago by h.mon25k
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Chip-Chip peaks calling
... Hi  I am new to ChIP-ChIP analysis. Can you please help me to understand which files from this experement are control samples and which ones are tratment?  (the organism is d.melanogaster)    Link to the data http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1283/samples/?s_sortby=col_39& ...
drosophila chip-chip written 3.8 years ago by marina-orlova70 • updated 3.8 years ago by Ian5.4k
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Chip-seq reads' trimming
... Hi all I have chip-seq reads of bad quality (dm3) - 29,772,199  reads:   Tried to trim it with fastq_quality_filter (command line fastq_quality_filter -q 20 -p 100 -i infile.fastq -o outfile.fastq) and got only 410,775 reads: Is that OK? Otherwise, what should I do to these data? I suppose I ...
chip-seq fastqc written 4.1 years ago by marina-orlova70 • updated 3.6 years ago by Biostar ♦♦ 20
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Comment: C: SRA to BAM
... Thank you for your answer, it helped ...
written 4.1 years ago by marina-orlova70
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Comment: C: SRA to BAM
... Hi Evgeniia Yes, you are right, it is raw reads. But fastq-dump also didn't work: fastq-dump SRR951914.sra > 951914.fastq 2015-04-08T08:50:36 fastq-dump.2.1.7 err: data bad version while constructing page map within virtual database module - failed SRR951914.sra Maybe sra archive is broken..  ...
written 4.1 years ago by marina-orlova70

Latest awards to marina-orlova

Great Question 16 months ago, created a question with more than 5,000 views. For Convert SAM to BAM
Popular Question 16 months ago, created a question with more than 1,000 views. For Chip-seq motif conservation
Supporter 16 months ago, voted at least 25 times.
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Chip-seq motif conservation
Popular Question 3.5 years ago, created a question with more than 1,000 views. For matchPWM problem, PSSM
Popular Question 3.5 years ago, created a question with more than 1,000 views. For average coverage, chip-seq
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Expression changes correlation
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Enrichment of ChiP over input comparison
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Differential binding analysis
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Isoforms' unique loci
Popular Question 3.5 years ago, created a question with more than 1,000 views. For alternative splicing analysis
Popular Question 3.5 years ago, created a question with more than 1,000 views. For MACS, effective genome size
Popular Question 3.5 years ago, created a question with more than 1,000 views. For macs and bedtools
Popular Question 3.5 years ago, created a question with more than 1,000 views. For chip-seq analysis (bowtie2, MACS2)
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Comparison of annotated genomes
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Chip-seq reads' trimming
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Alternative splicing analysis, rna-seq
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Convert SAM to BAM
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Diffbind bioconductor, peaks overlapping
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Quality control ChiP-Seq
Popular Question 4.0 years ago, created a question with more than 1,000 views. For chip-seq analysis (bowtie2, MACS2)
Scholar 4.6 years ago, created an answer that has been accepted. For A: matchPWM problem, PSSM

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