User: Ina

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Ina0
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Posts by Ina

<prev • 10 results • page 1 of 1 • next >
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Comment: C: NCBI blast remote on specific species
... Great! Looks cool. Thanks a lot! ...
written 9 months ago by Ina0
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Comment: C: NCBI blast remote on specific species
... Thank you! Is my below query correct to get an exact alignment for the fasta file? Each read has 23 nucleotides. blastn -query ../../Desktop/short_sample.fasta -db nt -remote -task blastn-short -word_size 23 -evalue 1 -perc_identity 100 -entrez_query "Homo sapiens [organism] AND GRCh37" -outfmt ...
written 9 months ago by Ina0 • updated 9 months ago by RamRS28k
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Comment: C: NCBI blast remote on specific species
... Hello, The query for doing a remote BLAST is very useful. Does anyone know how to specify the assembly type as well for Homo sapiens, say "grch37" or "hg19" in the query? ...
written 9 months ago by Ina0
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Comment: C: How to extract epigenetic features from ENCODE
... Thanks for your inputs [ATpoint][1] [1]: https://www.biostars.org/u/25721/ ...
written 9 months ago by Ina0
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Comment: C: How to extract epigenetic features from ENCODE
... Thanks a lot [jared.andrews07 ][1] [1]: https://www.biostars.org/u/40195/ ...
written 9 months ago by Ina0
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Comment: C: How to extract epigenetic features from ENCODE
... Is it possible for you to add a sample if it's not a trouble for you please. ...
written 9 months ago by Ina0
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Comment: C: How to extract epigenetic features from ENCODE
... Thank you @jared.andrews07 Do you mean the signal p-value? There are quite a few like "ENCFF145REP signal p-value rep 1" and "ENCFF118JQZ signal p-value rep 1,2" Which one should I look for? ![ENCODE sample][1] [1]: https://photos.app.goo.gl/my4keH3FJaXHBwiv9 ...
written 9 months ago by Ina0
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How to extract epigenetic features from ENCODE
... I am trying to use [ENCODE][1] to get epigenetic features like H3K4me3 position information and CTCF binding information from ChIP-Seq assay for a particular chromosome coordinate. I used the "search by region" option under "Data" in ENCODE to provide the coordinates like, for example for K562 cell ...
encode epigenetic written 9 months ago by Ina0 • updated 9 months ago by ATpoint36k
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Comment: C: Read alignment using Bowtie2
... Hi, Thank you [ATpoint][1] for your suggestion. So this is related to CRISPR-CAS9. I am working with off-target predictions for my thesis and was looking at all scientific papers related to CRISPR. I found one and decided to use their datasets. The datasets were not available directly and the me ...
written 11 months ago by Ina0
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Read alignment using Bowtie2
... Hello everyone! I am in need of using Bowtie2 to find all possible alignments for a set of reads (each 23bp long) to the human genome. The maximum number of mismatches that can be tolerated is 6. But since Bowtie2 allows mismatches only upto 1, I had to set the mismatch penalty for alignment score ...
bowtie2 alignment score written 11 months ago by Ina0 • updated 15 hours ago by Biostar ♦♦ 20

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