User: morteza.khabiri

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Posts by morteza.khabiri

<prev • 13 results • page 1 of 2 • next >
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Answer: A: massive pairwise sequence alignment
... I am answering my question, since It may help people with similar problem. The fast massive alignment is possible by applying Bowie. When you do alignment using Bowtie2 it will tell you how many sequences are repeated. And you can delete the repetitive sequences by extracting it from sam file (Bowti ...
written 9 weeks ago by morteza.khabiri0
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Comment: C: Split RNA-seq reads
... cutadapt -u 5 is also do the same job!!! ...
written 11 weeks ago by morteza.khabiri0
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Comment: C: massive pairwise sequence alignment
... Actually these sequences are not related to RNA-seq. I am trying to find unique sequences among a dataset with a million sequence then create a distance matrix based on that. ...
written 11 weeks ago by morteza.khabiri0
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Comment: C: massive pairwise sequence alignment
... Those softwares are deigned for multiple sequence alignment. right? But I dont want to do MSA. seq size ranges btw 100-300 bp. ...
written 11 weeks ago by morteza.khabiri0
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Comment: C: massive pairwise sequence alignment
... Thanks. I have already tried blast and the output is different than pairwise alignment!! ...
written 11 weeks ago by morteza.khabiri0
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massive pairwise sequence alignment
... Hi all, I have two sets of data (let's say A & B ) each includes 1000,000 sequences. I would like to see how many of sequences of one file (e.g. A) has at lease 90% matches to the sequences in the other file (e.g. B). I have already wrote a script which take one sequence from A and do pairwise a ...
alignment sequence written 11 weeks ago by morteza.khabiri0 • updated 9 weeks ago by jrj.healey3.9k
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Sringtie gff output has "STRG." instead of genid
... Hi all I am trying to do genome assembly by stringtie software. The command that I am using is as follow: - " stringtie -p 2 -G dmel.gtf -o out.gtf STAR.bam " - The input bam file is from STAR. The output file is look like this: 3R StringTie transcript 1 656 1 ...
assembly rna-seq written 3 months ago by morteza.khabiri0 • updated 3 months ago by genomax46k
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chipseq identified sequences
... HI All, I am not familiar with chip-seq data analysis. I would like to know why the chip-seq identified DNA sequences for one specific protein binding site has different lengths? for example the chipseq binding regions for protein A could be between 100-2000 bps? How the binding sites ranges determ ...
chip-seq written 3 months ago by morteza.khabiri0 • updated 11 weeks ago by arup230
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Answer: A: FIMO: scan motif on a DNA sequence
... Thanks .. It is very useful. But I meant the math behind motif discovery by having PWM and using HMM model. ...
written 3 months ago by morteza.khabiri0
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FIMO: scan motif on a DNA sequence
... Hi All, I am interested to understand how fimo (Find Individual Motif Occurrences ) works? In fact how PWM used as a prior information to find the probable motif occurrence in a DNA sequence? Unfortunately there is not enough description or computational method in FIMO original paper and I would be ...
genome statics alignment chip-seq written 3 months ago by morteza.khabiri0

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