User: nazaninhoseinkhan

Reputation:
240
Status:
Trusted
Location:
Iran, Islamic Republic Of
Last seen:
1 day, 5 hours ago
Joined:
4 years, 6 months ago
Email:
n****************@gmail.com

I am Nazanin Hosseinkhan, PhD in Bioinformatics. My background is Microbiology and I am seeking for a postdoc position.

Posts by nazaninhoseinkhan

<prev • 167 results • page 1 of 17 • next >
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Comment: C: problem in matching the names between file names and patients Id in TCGA
... I could get the full description of my files finally. Thank u all for your helps and comments ...
written 2 days ago by nazaninhoseinkhan240
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Comment: C: problem in matching the names between file names and patients Id in TCGA
... Hi Kevin, I run the code successfully. However I faced with another problem again. I have 1026 file names, however only 1020 IDs were found. More over I did not get the file names (AMAZE_p_TCGASNP_b86_87...seg.txt) in the results to map them to my original input. The results include file_id(fda02 ...
written 2 days ago by nazaninhoseinkhan240
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Comment: C: how to define different batches in DESeq2 in Galaxy
... Hi again, I found the solution Regards Nazanin ...
written 6 days ago by nazaninhoseinkhan240
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how to define different batches in DESeq2 in Galaxy
... Dear all, I have a RNASeq data set including tumor and healthy samples. However they have been collected from different laboratories. I want to know how should I define different laboratories as groups when using DESeq2. I have already performed this in R, however I want to do this in Galaxy thi ...
deseq2 batch effect removal rna-seq written 6 days ago by nazaninhoseinkhan240 • updated 6 days ago by ra0
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Comment: C: HTSeq-counts can not map any reads to gtf file
... Hi, Thank u for your reply The chromosome names are the same in both reference and gtf file: "chromosome". The out put of running IDxstats on my bam file was: 1 2 3 4 chromosome 6537648 1021248 0 * 0 0 2584368 I am pretty sure that I have mapped the reads since I had previously used the resul ...
written 7 days ago by nazaninhoseinkhan240
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HTSeq-counts can not map any reads to gtf file
... Dear all, I need to get the raw read counts of a *pseudomonas aeruginosa UCBPP-PA14 * RNASeq data set. After mapping with "Bowtie for Illumina", I run HTSeq-counts using 2 version of pseudomonas aeruginosa UCBPP-PA14 gft files obtained from ensembl and pseudomonas genome databases, however htseq-c ...
rna-seq htseq-counts no mapped reads written 7 days ago by nazaninhoseinkhan240 • updated 7 days ago by Friederike1.8k
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Comment: C: error in getting results from DESeq2
... Hi, Thank you so much for your reply. Yes, this morning I realized that I misspelled the "Condition". And thanks for your advice about maxit. I think it is about the number of iterations and does not affect my data. ...
written 8 days ago by nazaninhoseinkhan240
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Comment: A: error in getting results from DESeq2
... Yes, I got the error when I use "res <- results(dds, name="condition_Cancer_vs_normal")". I want to know what thresholds we are allowed to use in : keep <- rowSums((counts(dds)) >= 10) >=300 and in: dds <- nbinomWaldTest(dds, maxit=1000) ...
written 8 days ago by nazaninhoseinkhan240 • updated 8 days ago by Vijay Lakhujani2.5k
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error in getting results from DESeq2
... Dear all, I am trying to run DESeq2 to get the list of differential expressed miRNAs between 330 tumor and 42 normal samples. However when I run the following code: > dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ Condition) > dds <- estimateS ...
deseq2 error results written 9 days ago by nazaninhoseinkhan240 • updated 8 days ago by Devon Ryan80k
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Comment: C: problem in matching the names between file names and patients Id in TCGA
... Hi Kevin, Thank u so much. It worked I'll never forget your helps ...
written 12 days ago by nazaninhoseinkhan240

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