User: nikulina

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nikulina280
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280
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Location:
Cambridge
Last seen:
2 years, 7 months ago
Joined:
9 years, 1 month ago
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n***********@gmail.com

Posts by nikulina

<prev • 24 results • page 1 of 3 • next >
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Answer: A: Has anybody used TEToolkit successfully to quantify transposable elements?
... Hi! Do you have 'family_id' and 'class_id' in the 9th column of your gtf file? In my case adding those 'dummy' fields resolved the issue. ...
written 2.9 years ago by nikulina280
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Comment: C: Problem with qcovs in blast outfmt 6
... Thank you Peter, you saved me from insanity!  ...
written 4.2 years ago by nikulina280
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Comment: C: Where Can I Find Human Refseq That Come From The Same Transcription Locus?
... Thank you! Finally I used some perl programming to create merged intervals from the overlapping RefSeqs. ...
written 8.7 years ago by nikulina280
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Where Can I Find Human Refseq That Come From The Same Transcription Locus?
... Good day! Where can I find human refseq that come from the same transcription locus (gene) for hg18? So that refseq with overlapping coordinates are clustered into one gene? Is there any special database that can be downloaded? Thank you in advance! ...
refseq written 8.7 years ago by nikulina280 • updated 8.7 years ago by Andrew Su4.8k
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How To Process Large Chipseq Data?
... Good afternoon! I have a question concerning processing of large (~800 mb) raw Chipseq data . I have found CisFinder, but it is effective with sequences up to 50 Mb. Could you advise any tools (for windows) that will allow me to obtain peak coordinates? Thank you in advance. (The data of interes ...
chip-seq written 9.1 years ago by nikulina280 • updated 10 months ago by RamRS22k
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Answer: A: How To Find Any Of Many Motifs In Certain Sequences Using Perl?
... I eventually recognised how to modify my script to do the job I wished. Now it looks like the following:) $string_filename = 'seq.txt'; open(FILE, $string_filename) || die("Couldn't read file $string_filename\n"); $motif_filename = 'motif.txt'; open(MOTIF, $motif_filename) | ...
written 9.1 years ago by nikulina280 • updated 10 months ago by RamRS22k
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Comment: C: How To Find Any Of Many Motifs In Certain Sequences Using Perl?
... Thank you, I'll try to do something with it. ...
written 9.1 years ago by nikulina280
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Comment: C: How To Find Any Of Many Motifs In Certain Sequences Using Perl?
... I recognise that it is a problem but i haven't found the way to convert it to fasts yet. ...
written 9.1 years ago by nikulina280
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Comment: C: How To Find Any Of Many Motifs In Certain Sequences Using Perl?
... and the [genes](http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=162451049&hgSeq.promoter=on&boolshad.hgSeq.promoter=0&hgSeq.promoterSize=1000&hgSeq.utrExon5=on&boolshad.hgSeq.utrExon5=0&hgSeq.cdsExon=on&boolshad.hgSeq.cdsExon=0&hgSeq.utrExon3=on&boolshad.hgSeq.utrEx ...
written 9.1 years ago by nikulina280 • updated 10 months ago by RamRS22k
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Comment: C: How To Find Any Of Many Motifs In Certain Sequences Using Perl?
... the binding sites look like [this](ftp://ftp.ncbi.nlm.nih.gov/sra/Studies/SRP001/SRP001595/SRX015146/SRR032522.fastq.gz) ...
written 9.1 years ago by nikulina280 • updated 10 months ago by RamRS22k

Latest awards to nikulina

Popular Question 3.3 years ago, created a question with more than 1,000 views. For How To Find Paralogues?
Appreciated 6.6 years ago, created a post with more than 5 votes. For How To Find Paralogues?
Appreciated 6.6 years ago, created a post with more than 5 votes. For How To Parse Fasta Files In Perl
Great Question 6.6 years ago, created a question with more than 5,000 views. For How To Parse Fasta Files In Perl
Good Question 6.6 years ago, asked a question that was upvoted at least 5 times. For How To Parse Fasta Files In Perl
Epic Question 6.6 years ago, created a question with more than 10,000 views. For How To Parse Fasta Files In Perl
Popular Question 6.6 years ago, created a question with more than 1,000 views. For Where Can I Find Human Refseq That Come From The Same Transcription Locus?
Popular Question 6.6 years ago, created a question with more than 1,000 views. For How To Process Large Chipseq Data?
Popular Question 6.6 years ago, created a question with more than 1,000 views. For How To Find Any Of Many Motifs In Certain Sequences Using Perl?
Popular Question 6.6 years ago, created a question with more than 1,000 views. For How To Find Paralogues?
Popular Question 6.6 years ago, created a question with more than 1,000 views. For How To Parse Fasta Files In Perl
Supporter 6.6 years ago, voted at least 25 times.
Student 6.6 years ago, asked a question with at least 3 up-votes. For How Can I Find 1-And 2-Exone Genes?
Student 6.6 years ago, asked a question with at least 3 up-votes. For How To Process Large Chipseq Data?
Student 6.6 years ago, asked a question with at least 3 up-votes. For How To Find Paralogues?
Student 6.6 years ago, asked a question with at least 3 up-votes. For How To Parse Fasta Files In Perl

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