User: ej

gravatar for ej
ej60
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60
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Location:
European Union
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4 weeks ago
Joined:
5 years, 1 month ago
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Posts by ej

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Why is the hg38 exome so much bigger than hg19?
... Thank you for your reply. In the UCSC Table Browser I chose to download the NCBI RefSeq set for hg38, not the GENCODE. Is this not from the same source as the NCBI RefSeq in hg19? Where can I find RefSeq coordinates for hg38? ...
written 28 days ago by ej60
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Why is the hg38 exome so much bigger than hg19?
... Hi, I downloaded the NCBI Refseq curated file of Genes and Gene Predictions from the UCSC Table Browser for hg38 as I want to use the exon coordinates as a target file for calling variants on Exome Sequencing data. I noticed however, that the exon coordinates cover approximately double the genomi ...
exome hg38 refseq target written 28 days ago by ej60 • updated 28 days ago by vkkodali2.0k
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Comment: C: Bowtie2 - How can MAPQ be used to obtain uniquely mapped reads?
... That makes sense, thank you so much I really appreciate your help! ...
written 2.2 years ago by ej60
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Comment: C: Bowtie2 - How can MAPQ be used to obtain uniquely mapped reads?
... Also, from what I understand, AS is the alignment score of the read and XS is the score of the second best alignment. I used bowtie2 with default parameters so it is supposed to always choose the alignment with the best score, but I have some reads where the AS is lower than the XS. Why would this b ...
written 2.2 years ago by ej60
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Comment: C: Bowtie2 - How can MAPQ be used to obtain uniquely mapped reads?
... Thank you so much for your help. Do you know of an example when a read has multiple alignments but will not have the XS tag? ...
written 2.2 years ago by ej60
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Bowtie2 - How can MAPQ be used to obtain uniquely mapped reads?
... Hi, I am interested in extracting uniquely mapped reads from a bam file by filtering based on the MAPQ field. I ran some tests to figure out what MAPQ threshold should be used but am having trouble understanding the results. I ran bowtie2 on paired-end data and saw that when the reads are uniqu ...
alignment chip-seq sequencing written 2.2 years ago by ej60 • updated 2.2 years ago by Kevin Blighe59k
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Comment: C: Chip-Seq - How to do Quantile normalization on bam files?
... Thank you so much ...
written 4.5 years ago by ej60
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Chip-Seq - How to do Quantile normalization on bam files?
... Hi, I am working with ChIP-Seq data and am interested in doing quantile normalization. I created bedgraph files from my bam files using bamCoverage with a window size of 50 bp so that I get the number of reads for every 50 bp of genome. However I noticed that every bam file has a different number ...
normalization bam chip-seq written 4.5 years ago by ej60 • updated 4.5 years ago by James Ashmore2.9k
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Chip-Seq - Peak caller for broad enrichment of histone modifications?
...  I'm analyzing Chip-Seq data and am interested in histone modifications that have very broad peaks such as H3K27me3 and H3K36me3. I have tried peak calling using Homer but it does not seem to work well. Is there a better peak caller for these modifications that have broad enrichment across the genom ...
chip-seq written 5.1 years ago by ej60 • updated 4.0 years ago by Ming Tang2.6k

Latest awards to ej

Great Question 2.2 years ago, created a question with more than 5,000 views. For Chip-Seq - Peak caller for broad enrichment of histone modifications?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Chip-Seq - How to do Quantile normalization on bam files?
Appreciated 4.4 years ago, created a post with more than 5 votes. For Chip-Seq - Peak caller for broad enrichment of histone modifications?
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Chip-Seq - How to do Quantile normalization on bam files?
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Chip-Seq - Peak caller for broad enrichment of histone modifications?
Student 4.4 years ago, asked a question with at least 3 up-votes. For Chip-Seq - Peak caller for broad enrichment of histone modifications?

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