User: ebrahimiet

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ebrahimiet40
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Posts by ebrahimiet

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Comment: A: database for enhancer sequences in human/mammal genomes
... many thanks for the link ...
written 10 days ago by ebrahimiet40
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database for enhancer sequences in human/mammal genomes
... Hi, can anyone introduce database/collection ofr enhancer sequences and their annotations for human/mammal genomes to be used in analyses such as chipseq many thanks ...
chip-seq written 10 days ago by ebrahimiet40 • updated 10 days ago by Grinch0
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Alignment score in relation to lenght
... Hi all, How alignment score is defined in relation to the length of adaptor (sequence to be alligned)? For example, if our adaptor is 30bp, we need to increase alignment score, compared to the time which adaptor is 20 bp? many thanks ...
alignment written 19 days ago by ebrahimiet40
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Trimming Adaptor in Small RNA Analysis
... Hi, I have new Small RNA sequencing generated by Illumina machine (Nextseq). This Small RNAseq data is generated by “TruSeq Small RNA” library preparation kit. I have the “Illumina Customer Sequence Letter” from the link (https://support.illumina.com/downloads/illumina-customer-sequence-letter.htm ...
rna-seq written 19 days ago by ebrahimiet40
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How many lanes does the Nextseq (illumina) flow cell have?
... Hi all, How many lanes does the Nextseq (illumina) flow cell have? Thanks. ...
sequencing written 20 days ago by ebrahimiet40 • updated 20 days ago by Petr Ponomarenko1.2k
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Illumina adaptor to be trimmed from fastq RNAseq files
... Hi Which Adaptor (and any other sequence) needs to be trimmed from RNASeq fastq data generated by Illumina TruSeq stranded mRNA Sample Preparation kit Thanks ...
rna-seq written 8 weeks ago by ebrahimiet40
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Is Ion Torrent technology acceptable for meta-genomics to profile microbiome?
... Dear all, Is Ion Torrent technology acceptable for meta-genomics to profile microbiome? or we have to use only Illumina platforme? for meta-genome, short reads are better or paired reads? Which lenght of short reads and which depth you suggest? Is it different between whole sequencing or 16S? Th ...
next-gen written 7 months ago by ebrahimiet40
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Answer: A: optimum number of short reads for denovo assembly
... For 60x coverage of 15 kb genome, how many paired short reads in 250 bp reads I should use? how many paired short reads in 150 bp reads I should use? Which formula converts the the length and number of short reads to coverage base on genome size? thanks ...
written 7 months ago by ebrahimiet40
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optimum number of short reads for denovo assembly
... Dear all, I am running denovo assembly for Newcastle (NDV) virus which its genomic size is 15 kb. What is the optimum number of Illumina paired end short reads to start denovo assembly with 250 bp reads? 150 bp reads? many thanks Esmaeil ...
assembly written 7 months ago by ebrahimiet40 • updated 7 months ago by dbrowne.up50
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Answer: A: Machine learning features from nucleotide sequences
... In the following papers, we used a range of nucleotide features Gene Volume 578, Issue 2, 10 March 2016, Pages 194–204 Unravelling evolution of Nanog, the key transcription factor involved in self-renewal of undifferentiated embryonic stem cells, by pattern recognition in nucleotide and tandem repe ...
written 7 months ago by ebrahimiet40

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