User: biorepine

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biorepine1.4k
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Posts by biorepine

<prev • 133 results • page 1 of 14 • next >
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How to rescale aggregation plots of different ChIP-seq datasets using ngsplot?
... Hi, As you can see here, H3K4me3 has higher signal compared to the rest (probably because of more reads). RPM method (Read count per million mapped reads) should take care of this but it seems not. So, Is there a way, I can re-scale the plots (using log scale for example) so that I can compare thes ...
chip-seq written 2.0 years ago by biorepine1.4k
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What is the best way to find broad ChIP-Seq peaks using a BAM file with 600 million reads?
... Dear Biostars, I generally use MACS program to identify broad peaks directly from a BAM file (without worrying about converting BAM into something else). However, it is still time consuming when I run it on a file with many sequencing reads (in my case 600 million reads). Is there any faster approa ...
macs chip-seq written 2.3 years ago by biorepine1.4k
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Comment: C: How to calculate fraction of RNA-Seq reads mapped to a customised genomic locati
... but htseq-count doesn't have -f option? ...
written 2.9 years ago by biorepine1.4k
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Comment: C: How to calculate fraction of RNA-Seq reads mapped to a customised genomic locati
... Does this work ? samtools sort file1_mapped.bam - |samtools view -bf 1 - |samtools view - | python htseq-count --mode=union --stranded=no - gtf.file ...
written 2.9 years ago by biorepine1.4k
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How to calculate fraction of RNA-Seq reads mapped to a customised genomic locations?
... Dear Biostars, I am trying to calculate the fraction of RNA-Seq reads map to a customised dataset of genomic locations. I am using the following steps. Could you please answer whether this is correct or not? Also do you think is there any better or fatser way to do this? Data: BAM file (Paired-end ...
rna-seq written 2.9 years ago by biorepine1.4k • updated 2.9 years ago by WouterDeCoster40k
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Comment: C: How One Can Separate Noncoding From Coding Ucsc And Ensembl Transcripts
... So if I change cdsStart!=cdsEnd, does it print only coding genes ? Thanks ...
written 4.4 years ago by biorepine1.4k
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SRX from SRR IDs
... Does any one know how to extract SRX ids from SRR ids. Thanks. ex: input  SRR1294518 output SRR1294518  SRX549132   ...
sra written 4.6 years ago by biorepine1.4k • updated 2.2 years ago by James Ashmore2.6k
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Comment: C: Quick way to find all the TFBS peak data for mouse and Human in GEO
... you better do some googling first. here is the post where it already has been asked https://www.biostars.org/p/15798/ ...
written 4.7 years ago by biorepine1.4k
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Comment: C: How To Download All Sra Samples At Once ?
... Yes but I already downloaded and processed large number of SRA samples. All I want to do is rename them with proper GEOid. I didn't see any information on this in either of the packages :( ...
written 4.7 years ago by biorepine1.4k
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Comment: C: How To Download All Sra Samples At Once ?
... Hi, it is working great! However, I couldn't find a way to retrieve the information (ex: A specific tissue RNA-Seq) that related to specific SRA number. They are usually marked by GSE ids rather than SRA ids. Any suggestions would be appreciated!  ...
written 4.7 years ago by biorepine1.4k

Latest awards to biorepine

Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Downloading All Cshl Long Rna Seq Data From Ucsc Ftp Server
Appreciated 15 months ago, created a post with more than 5 votes. For A: What Do You Waste Your Time On
Popular Question 2.0 years ago, created a question with more than 1,000 views. For SRX from SRR IDs
Popular Question 2.0 years ago, created a question with more than 1,000 views. For How To Overlap Human And Mouse Genomic Regions (Ex: Chip-Seq Peaks)
Prophet 2.0 years ago, created a post with more than 20 followers. For How To Download All Sra Samples At Once ?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Where Can I Download Most Updated Cnvs Of Hg19 ?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Should I Use Strand Info, When I Overlap Snps With Genes ?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For iGenome indexes for Chimpanzee and Bonobo (panTro3)
Popular Question 2.0 years ago, created a question with more than 1,000 views. For How To Split Chr11 Bam File In To 2 Halves ?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Where Can I Download Pirna (Piwi Rnas) Of Mouse (Mm9)
Great Question 2.1 years ago, created a question with more than 5,000 views. For How To Extract Scores From Bedgraph File Using Bed Tools
Prophet 2.1 years ago, created a post with more than 20 followers. For How Do You Justify Your Rna-Seq Expression Threshold (Fpkm/Rpkm) ?
Student 2.1 years ago, asked a question with at least 3 up-votes. For Where Can I Download Most Updated Cnvs Of Hg19 ?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How To Overlap Human And Mouse Genomic Regions (Ex: Chip-Seq Peaks)
Good Question 2.7 years ago, asked a question that was upvoted at least 5 times. For What If Authors Do Not Share Their Published Data ?
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: What Do You Waste Your Time On
Student 2.7 years ago, asked a question with at least 3 up-votes. For What If Authors Do Not Share Their Published Data ?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How One Can Separate Noncoding From Coding Ucsc And Ensembl Transcripts
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Fr-Secondstrand Versus Fr-Unstranded Library Type In Tophat2
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How To Overlap Human And Mouse Genomic Regions (Ex: Chip-Seq Peaks)
Epic Question 2.8 years ago, created a question with more than 10,000 views. For How Do You Justify Your Rna-Seq Expression Threshold (Fpkm/Rpkm) ?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For How To Download All H3K27Me3 Chip-Seq Datsets Of Mouse At Once
Epic Question 3.6 years ago, created a question with more than 10,000 views. For How To Convert Gencode Gtf Into Bed Format ?
Prophet 3.6 years ago, created a post with more than 20 followers. For How Do You Justify Your Rna-Seq Expression Threshold (Fpkm/Rpkm) ?
Great Question 3.6 years ago, created a question with more than 5,000 views. For How To Convert Gencode Gtf Into Bed Format ?

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