User: mirzaei86.vahid

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Posts by mirzaei86.vahid

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Comment: C: Having multiple adapter sequence in raw fastq files?
... thanks for your helps. ...
written 2.4 years ago by mirzaei86.vahid30
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Comment: C: Having multiple adapter sequence in raw fastq files?
... thanks @genomax2, how can I crop first 13 bases from start of reads?? ...
written 2.4 years ago by mirzaei86.vahid30
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Answer: A: what is the meaning of 'Species ID' in targetscan?
... You could find [here][1] information about tax/species ID. **Human id is =9606** You could google it before asking such question. [1]: https://www.ncbi.nlm.nih.gov/taxonomy/9606 ...
written 2.4 years ago by mirzaei86.vahid30
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Having multiple adapter sequence in raw fastq files?
... Dear all, I have 50 RNA-Seq samples for a project. FastQC reports different **TruSeq Adapter, Indexes (mostly 2, 7,5 and 14)** for each of them and also some of them might have **llumina Single End PCR Primer 1**. I see very good quality score (>30 for most of reads) but there were fluctuation ...
next-gen rna-seq written 2.4 years ago by mirzaei86.vahid30
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What is ploidy level for HaplotypeCaller ?
... Dear all, I have rudimentary questions about **GATK** pipline: First about **HaplotypeCaller** , I have set **-ploidy 1** , my sample belong to human specie. Is it correct to set ploidy=1 for human? I'm working on germline mutation but I saw different pipeline for somatic mutation in [GATK bes ...
genome gatk snp written 2.4 years ago by mirzaei86.vahid30 • updated 2.4 years ago by WouterDeCoster40k
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How to read multiple samples with DESeq2?
... Hello I have a count file which has multiple columns, (one column for one sample). As I found, In DESeq2 we should insert count files separately. Is it possible to insert one file with multiple columns? like below: Gene Sample1 Sample2 g1 22 0 g2 5 ...
R deseq2 rna-seq written 2.4 years ago by mirzaei86.vahid30 • updated 2.4 years ago by ivivek_ngs4.8k
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Comment: C: What is present and absent calling in high-throughput data?
... dear Nazanin, my data is expression profile. ...
written 2.4 years ago by mirzaei86.vahid30
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Comment: C: What is present and absent calling in high-throughput data?
... thanks @mastal511, it is expression data. and from 1700 have 0 value from 33K gene ids. So I should cut 0 value? ...
written 2.4 years ago by mirzaei86.vahid30
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Answer: A: Meaning of Per sequence quality scores in FastQC
... Dear Somayeh Per sequence quality shows overall read count for each quality scores, for example if you got highest peak for "30" it means Q30 have more read number than other quality scores. X axes = Quality scores and Y axes= Number of reads. To get me more information please take a brief look at ...
written 2.4 years ago by mirzaei86.vahid30
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What is present and absent calling in high-throughput data?
... Hi I have an expression dataset, It has a column entitled absent/present calling (values 0 or 1), I have two questions: 1- Should I treat different on expression columns based on 0 or 1 ? 2- Is this column just used for Microarray or it could be used for RNA-SEQ too? Thanks. ...
R microarray rna-seq written 2.4 years ago by mirzaei86.vahid30 • updated 2.4 years ago by nazaninhoseinkhan370

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