User: valerie

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valerie60
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11 months, 1 week ago
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2 years, 4 months ago
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Posts by valerie

<prev • 68 results • page 1 of 7 • next >
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Comment: C: Find reads that completely cover short sequences
... The main issue is that when I am using bowtie2 in default mode it doesn't map anything at all to sequences that are shorter then reads. When I try local mode, I get something that is difficult to analyse, because there are a lot of very short alignments. I was wondering if there is a simple way. ...
written 11 months ago by valerie60
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Comment: C: Find reads that completely cover short sequences
... Sorry, didn't get your question. It's fasta. ...
written 11 months ago by valerie60
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Comment: C: Find reads that completely cover short sequences
... I have an index of ~100 of short sequences I am mapping to ...
written 11 months ago by valerie60
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Find reads that completely cover short sequences
... Hi everyone, I have WGS with paired-end reads length of 100 and several reference sequences length of ~70. I want to find those reads (not pairs, just single reads) which completely cover short sequences, i.e. those reads that map to short sequences so that whole sequence is inside this read. How c ...
wgs bowtie2 written 11 months ago by valerie60 • updated 11 months ago by Jeffin Rockey1000
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Comment: C: Identification of short insertions in genome
... Thank you very much for your help, Brian! ...
written 19 months ago by valerie60
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Comment: C: Identification of short insertions in genome
... Brian, thank you so much for your explanation! May I ask you one more question? Actually I am looking for new copies of repetitive elements in cancer genomes. I suppose that tumors are mosaic and I want kind of "measure" the activity of transposition process not identify precisely each insertion. Th ...
written 19 months ago by valerie60
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Comment: C: Identification of short insertions in genome
... Dear Brian, Could you please explain in few words what is going on here? Should I add my sequences of interest to reference genome in genome.fa to use the first option? Thank you! ...
written 20 months ago by valerie60
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Comment: C: Identification of short insertions in genome
... Great! Thank you, Tim! ...
written 20 months ago by valerie60
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Comment: C: Identification of short insertions in genome
... Thank you! Actually they are almost the size of a read (~230 nucl), is it a small indel? ...
written 20 months ago by valerie60
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Identification of short insertions in genome
... Hi guys, I need to identify insertions of specific sequences in my genomes. I have WGS data with read length of 250 nucl. Previously I was working on identification of large sequences insertions and simply looked for discordantly mapped reads for that using bowtie2 and bbmap. Now I am looking for ...
wgs alignment written 20 months ago by valerie60 • updated 18 months ago by Biostar ♦♦ 20

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Supporter 20 months ago, voted at least 25 times.

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