User: haewon

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haewon0
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Posts by haewon

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Comment: C: How can I extract position information from multiple alignment format?
... Yes, that's exactly what I'm looking for. I'll take a look for biopython. Thanks for the suggestion. ...
written 9 months ago by haewon0
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Comment: C: How can I extract position information from multiple alignment format?
... Thanks for your suggestion. I tried bowtie2 and bwa but both of them couldn't identify the gap even with 0 gap opening and gap penalty - they instead clipped the sequence. And then I also tried blastn but it gave 2 results matching only 5' or 3'. ...
written 9 months ago by haewon0
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How can I extract position information from multiple alignment format?
... Hi I have generated simple multiple alignment files using MAFFT. mafft --clustalout mafft_input.txt > mafft_output.txt And below is the output file Is there anyway I can get position information of matching or deleted region? Thanks in advance. ...
multiple alignment clustal mafft written 9 months ago by haewon0
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Comment: C: blast with large deletion
... mafft and muscle both work very well. However, I need to get more like machine readable output format something like you can get using -outfmt 6 in blastn. Below is my example code and output format. blastn -db ~/data/raw/GSKOampliconNGS/IntronGSgene.fa -query test.fa -out test_results.out -out ...
written 9 months ago by haewon0
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Comment: C: blast with large deletion
... Thanks! I'll try them. ...
written 9 months ago by haewon0
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blast with large deletion
... Hi, I'm trying to align some sequences that have large deletion (~150bp) using command line blastn. Size of subject is 266bp and query size is about 115bp. Blastn can align the query either to 5' end or 3' end of the subject but it cannot align the query as a single alignment with large gap. I tri ...
blast deletion written 9 months ago by haewon0 • updated 9 months ago by h.mon31k
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Comment: C: How to identify 100ish deletion from NGS data
... Any recommendation for splice aware aligner? I searched and found only RNA-seq aligners including STAR and Tophat2. I couldn't figure out how I can use these tools with DNA-seq data. ...
written 10 months ago by haewon0
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Comment: C: How to identify 100ish deletion from NGS data
... I have never thought that way and realized that blast is quite good at handling large deletion. Thanks for the suggestion. ...
written 10 months ago by haewon0
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Comment: C: How to identify 100ish deletion from NGS data
... Thanks for your input. 1. Targeted sequencing means NGS sequencing(MySeq) of PCR amplicon. Because I know approximately what my sequences are, I thought I don't really need to map them to entire genome. 2. I have already screened my clones with PCR. Since there is a large deletion (100bp) it was e ...
written 10 months ago by haewon0
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How to identify 100ish deletion from NGS data
... Dear Biostars, I generated knock-out cell lines using CRISPR-Cas9 with 2 sgRNAs targeting 100bp apart. Then I identified knockout clones by PCR. Instead of sequencing all 75 clones, I decided to combine all clones together and send samples for targeted sequencing. I mapped the reads to the region o ...
crispr targeted sequencing written 10 months ago by haewon0

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