User: noushin.farnoud

gravatar for noushin.farnoud
Reputation:
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Location:
United States
Last seen:
2 months, 2 weeks ago
Joined:
4 years, 9 months ago
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Posts by noushin.farnoud

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Problem with bcftools roh
... @kevin Thanks a lot. I came across that in searches, will give it try. Thanks again for your help and input! ...
written 8 months ago by noushin.farnoud100
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Comment: C: Problem with bcftools roh
... The distance between variants is something I did not take into consideration! The reason that there are 309 variants is that I wanted to query LOH only on a specific chromosome (chr 9) and also I am working with a targeted assay. So what I did was finding all dbSNP snps that fall within my assay's . ...
written 8 months ago by noushin.farnoud100
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Comment: C: Problem with bcftools roh
... Yes, it's puzzling. No error. But as noted in the stdout (last line of the block above) it says 2 (out of 309) lines are processed with no further explanation: **Number of lines: total/processed: 309/2** ...
written 8 months ago by noushin.farnoud100
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Problem with bcftools roh
... Dear All, I have a problem with **bcftools roh** and hope you can guide me to what may be causing this: I run **Example-1** of the Github: http://samtools.github.io/bcftools/howtos/roh-calling.html and see the output consists of a state (0:HW, 1:AZ) , and quality **for each position that was in t ...
homozygosity roh bcftools written 8 months ago by noushin.farnoud100
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Comment: C: "first magic byte doesn't match" error in FusionMap
... Thanks. In fact when I gzipped the data, the error was gone. Now I have an understanding what "first magic byte error" was referring to!  ...
written 4.0 years ago by noushin.farnoud100
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"first magic byte doesn't match" error in FusionMap
... Dear BioStars, I am trying to run FusioMap to detect candidate fusions in a paired end RNASeq data set. I have already tested this dataset with a few other fusion algorithms and received no error (so am sure the .fastq files are not corrupted). But when running with FusionMap I get this error.  I h ...
fusion fusionmap rna-seq written 4.0 years ago by noushin.farnoud100 • updated 4.0 years ago by Jean-Karim Heriche21k
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Problem with creating GSEA rank file
... Dear Biostars, I want to prepare the rank file for GSEA analysis based on RNA-seq results that were generated by DESeq2.  I have  found different recommendations as how to create the pre-ranked gene list. The GSEA site mentions the gene list can be sorted by any value, however, other people have po ...
gsea rna-seq written 4.1 years ago by noushin.farnoud100
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Sample clustering in RNASeq
... Dear BioStars, One of the methods for data quality assessment suggested in DESeq2 is to apply sample clustering. I have an RNASeq experiment with 8 treated and 6 untreated samples. All samples have good data quality metrics according to FastQC. But when I plot the heatmap of "rlog" transformed data ...
rnaseq deseq2 myposts heatmap written 4.2 years ago by noushin.farnoud100
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How to remove reads associated with a specific region from bam file?
... Dear Members,  Is there a way I can removes reads associated with a region (chr, start, end) from a .bam file (RNASeq data) prior to the application of HTSeq? I will greatly appreciate your feedback, Noushin ...
alignment samtools rna-seq written 4.5 years ago by noushin.farnoud100 • updated 3.0 years ago by Ron980
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issue with VISTA enhancer database
... Dear BioStars, I want to download the list of candidate enhancer for mouse from VISTA database. As you can see in the link below, the presented list also includes the flanking gene information: http://enhancer.lbl.gov/cgi-bin/imagedb3.pl?show=1;page=1;form=search;search.form=no;page_size=100;search ...
chip-seq written 4.5 years ago by noushin.farnoud100 • updated 4.5 years ago by Ryan Dale4.8k

Latest awards to noushin.farnoud

Great Question 6 months ago, created a question with more than 5,000 views. For Problem with creating GSEA rank file
Popular Question 20 months ago, created a question with more than 1,000 views. For Sample clustering in RNASeq
Popular Question 20 months ago, created a question with more than 1,000 views. For issue with VISTA enhancer database
Popular Question 20 months ago, created a question with more than 1,000 views. For Unexpected RNASeq result in shRNA experiment
Student 20 months ago, asked a question with at least 3 up-votes. For Problem with creating GSEA rank file
Popular Question 23 months ago, created a question with more than 1,000 views. For Sample clustering in RNASeq
Great Question 2.3 years ago, created a question with more than 5,000 views. For What is the acceptable % of reads that map to no feature (in RNASeq)?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How to remove reads associated with a specific region from bam file?
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Problem with creating GSEA rank file
Popular Question 3.7 years ago, created a question with more than 1,000 views. For How to remove reads associated with a specific region from bam file?
Popular Question 3.7 years ago, created a question with more than 1,000 views. For What is the acceptable % of reads that map to no feature (in RNASeq)?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For What is the acceptable % of reads that map to no feature (in RNASeq)?

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