User: mehran.karimzade

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Posts by mehran.karimzade

<prev • 36 results • page 1 of 4 • next >
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Answer: A: Which one do I need to consider single-read or multi-read mappability bigwig fil
... I hope you found the answer to your questions by now but since this post still remains unanswered: Mappability of the genome depends on how you sequence it. If it's paired, unpaired, and what read lengths you used for sequencing. For example, if you used unpaired 100 bp reads to sequence your geno ...
written 9 months ago by mehran.karimzade160
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Comment: C: Where can I find CCLE RNAseq BAM files?
... I don't see this added yet. Any link or update yet? ...
written 16 months ago by mehran.karimzade160
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Answer: A: calculate mappability score for each window
... You can use per-base mappability tracks of hg19 for several common short-read sequencing read lengths (24, 36, 50, and 100) from http://bismap.hoffmanlab.org/. You can download the files in wiggle or BED. ...
written 23 months ago by mehran.karimzade160
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Answer: A: Heatmap of enriched GO terms in R
... A hierarchical clustering can be made by various approaches where you first calculate a distance matrix (which you can use different approaches such as euclidean distance, 1-pearson correlation, etc.) and then choose a clustering method (complete, ward, etc.). In your case it would be better to in ...
written 3.2 years ago by mehran.karimzade160
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Answer: A: How to convert a whole genome gene position reference number (ID) list to the a
... Make sure our file is sorted and the first 3 columns of your file are: chromosome name | start position | end position You would need to download a file from [ENSEMBL biomart](http://useast.ensembl.org/biomart/martview/b70e259ff334a0ab92641696a32bd5a2) for your genome of interest that starts with f ...
written 3.3 years ago by mehran.karimzade160
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Answer: A: Help with adding a row color side bar using pheatmap??
... I executed your script and dimensions of your *categoriesrow* are 10X2 and you cannot specify 10 column names to a dataframe with 2 columns. Change this: colnames(categoriesrow) <- rownames(dummymat) to: rownames(categoriesrow) <- rownames(dummymat) Would work. ...
written 3.3 years ago by mehran.karimzade160
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Answer: A: List of Ensembl Transcript IDs corresponding to protein-coding genes
... Go to: http://www.ensembl.org/biomart/martview/21893b6a5bf91112c9a786f296b9200d Choose database > Ensembl Gene 83 > Homo sapiens Attributes > Gene > click on Ensembl Protein ID (or any other protein IDs such as refseq, etc.) go to results and download   ...
written 3.4 years ago by mehran.karimzade160
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Comment: C: CNVnator histogram error
... It is weird if you get the exact same error after adjusting the chromosome size in sam headers. Apparently no bed. You may want to try the fix here if something is weird with your bam file: https://github.com/abyzovlab/CNVnator/issues/12 and if this doesn't work, I would post it in their github i ...
written 3.5 years ago by mehran.karimzade160
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Answer: A: CNVnator histogram error
... The length of chromosome 18 is 78077248 but in your input you have a region ending in 78077249. Do use a bed format at some point? It seems that you are using 1 based system instead of a 0 based system. If the data is in bed format, subtract 1 from the end positions. If the input data is in BAM f ...
written 3.5 years ago by mehran.karimzade160
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Comment: C: SPIA - How to update and integrate new KEGG pathways????
... GprofileR to my knowledge uses the most up to date KEGG, Reactome, GO and etc. pathway analysis http://biit.cs.ut.ee/gprofiler/ ...
written 3.7 years ago by mehran.karimzade160

Latest awards to mehran.karimzade

Popular Question 15 months ago, created a question with more than 1,000 views. For Black color reads in IGV: bwa-meth
Popular Question 23 months ago, created a question with more than 1,000 views. For Black color reads in IGV: bwa-meth
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Black color reads in IGV: bwa-meth
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Acquiring Chromosomal Location (Cytoband) For A Large Set Of Genes
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Acquiring Chromosomal Location (Cytoband) For A Large Set Of Genes
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Retrieving All Uniprot/Gene Ids From Bioconductor Biomart
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: List of Ensembl Transcript IDs corresponding to protein-coding genes
Scholar 3.4 years ago, created an answer that has been accepted. For A: Bismark .cov coverage underrepresentation
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Acquiring Chromosomal Location (Cytoband) For A Large Set Of Genes
Scholar 3.7 years ago, created an answer that has been accepted. For A: Bismark .cov coverage underrepresentation
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Acquiring Chromosomal Location (Cytoband) For A Large Set Of Genes
Scholar 4.2 years ago, created an answer that has been accepted. For A: Bismark .cov coverage underrepresentation

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