User: blur

gravatar for blur
blur110
Reputation:
110
Status:
Trusted
Location:
European Union
Last seen:
6 days, 11 hours ago
Joined:
4 years, 6 months ago
Email:
b***@pazcorp.com

Posts by blur

<prev • 120 results • page 1 of 12 • next >
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Comment: C: DB for small RNAs in plant genomes?
... thanks! that's great :) ...
written 7 days ago by blur110
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DB for small RNAs in plant genomes?
... Hi, I am looking for a database of small RNAs (snoRNAs, snRNAs, mirs) in plant genomes. Does anyone know of such a DB? I know there are such DBs for human small RNAs. I know mirbase and mirtarbase, but looking for other small RNAs (preferably bed files of genomic locations if anyone knows where to ...
db small rna written 7 days ago by blur110
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Comment: C: How do I know if I have DNA contamination in RNA-seq data?
... Thanks, I'll try it all (the library is after experimental rRNA depletion, but I guess it never hurts to check again) ...
written 4 months ago by blur110
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How do I know if I have DNA contamination in RNA-seq data?
... Hi, I want to know whether I have DNA contamination in my RNA-seq data. I have a library with DNAse and one without DNAse and another pair with additional treatment [DNAse(+) vs. DNAse(-), DNAse(+)+X vs. DNAse(-)+X] I tried: 1) Checking overall alignment rate of DNAse(+) vs. DNAse(-) and DNAse(+ ...
contamination rna-seq written 4 months ago by blur110
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Comment: C: bad quality in certain tiles according to "Per tile sequence quality" in FASTQC
... I do think there was a sequencing problem... I will try and clean it using the tools suggested Thanks ...
written 4 months ago by blur110
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Comment: C: bad quality in certain tiles according to "Per tile sequence quality" in FASTQC
... There is phiX, but it can't be the reason as all the runs have phiX... Also, the quality is clearly affected as the errors bars of the reads are very, very long ...
written 4 months ago by blur110
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bad quality in certain tiles according to "Per tile sequence quality" in FASTQC
... Hi, I have been looking at a library run in Hiseq using fastQC. Usually I get good Per tile sequence quality, with the entire area looking bluish (OK quality throughout). But this time I get tiles that appear to give consistently low quality reads over the entire read sequence. The thing is - I tho ...
fastqc per tile sequence quality written 4 months ago by blur110
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Comment: C: Filtering noise out of SAM file using CIGAR
... thanks! I'll try this ...
written 7 months ago by blur110
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Comment: C: Filtering noise out of SAM file using CIGAR
... regretfully, it is an actual example from my SAM file. Any pointers as how to change my BWA mem options to get rid of these? Thanks, ...
written 7 months ago by blur110
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Comment: C: RNA-seq alignment rate is too low.
... Have you tried using a mir reference? i.e. a reference only containing the mirs sequences? You can use MiRbase download to get this data: http://www.mirbase.org/ftp.shtml ...
written 7 months ago by blur110

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Popular Question 4 months ago, created a question with more than 1,000 views. For Generate consensus from BAM file
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Popular Question 11 months ago, created a question with more than 1,000 views. For R1 and R2 in sequencing data
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Centurion 13 months ago, created 100 posts.
Popular Question 15 months ago, created a question with more than 1,000 views. For Generate consensus from BAM file
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