User: ori

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ori50
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Posts by ori

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Comment: C: How to improve alignment quality of ChIP-seq for single-end
... Check the unmap reads (e.g. BLAST search), and you will find the reason why they have not aligned to the reference genome. * bowtie2 "--un" option will write reads that fail to align. ...
written 4 months ago by ori50
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Answer: A: Identify protein sequences from L.infantum with more than 60% conservancy with o
... First, it is necessary to clarify the definition of “60% of conservancy” (e.g. 60% similarity across 90% of the protein sequence). Next, try BLASTP with additional -outfmt options, “pident” and “qcovs”. You will get results with pident (% of identical matches) and qcovs (query coverage per subject) ...
written 4 months ago by ori50
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Comment: C: Error in Generating sorted.bam
... Could you get the dustMapping.sam that is the first output file? If not, please check whether there are bowtie"2" index files near the reference file (pavelAssemblyBowtieIndex .fa). Bowtie2 index : .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, and .rev.2.bt2. Bowtie 2's .bt2 index format is different ...
written 4 months ago by ori50
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Answer: A: Map eukaryotic genomic reads to transcript reference of closely related organism
... I think it is difficult to align genomic reads from A to transcripts of B by bowtie, because similarity between the two genomes (70%) is too low to align short reads. Instead, how about below analysis? 1) De novo assembly of genomic reads from A 2) BLASTn or tBLASTx search; query = transcript s ...
written 4 months ago by ori50
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Comment: A: SNP Analysis of bacterial genomes
... Are the species of two acinetobactor same? Are there reference genomes of the species in database? It is important to define what genomes you want to compare to detect SNPs. Once that is decided, you will be able to refer to the tools described by ropolocan. ...
written 4 months ago by ori50
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Answer: A: Integrated DNA and RNA sequences in expression analysis
... What is the organism? Is not the genome of the organism has been determined? We often use only RNA-Seq data to analyze gene expression, because molecules expressed from genes are RNA. Would you tell us why you have sequenced genome DNA for expression analysis? ...
written 4 months ago by ori50
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Answer: A: Research papers or articles to gain knowledge about fastqc tool,fastx toolkit,an
... FastQC, FASTX toolkit and cutadapt do not execute the algorithm developed taking into consideration biological implications, but are simple tools that evaluate or edit reads from NGS. I suggest the best way to know how to use is to see manuals of the tools. Instead, if you want to cite the tools fo ...
written 4 months ago by ori50
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Answer: A: making a custom reference
... I think SNP is at the base position that the base in one genome (ex: genome A) is different from the base in the other genome (ex: genome B).From your question, it seems that the reads derived from genome A and genome B are mixed in the data, and genome A = sequences produced by some selected reads; ...
written 4 months ago by ori50

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