User: Ravi Karra

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Ravi Karra140
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Posts by Ravi Karra

<prev • 13 results • page 1 of 2 • next >
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Comment: C: dba.counts error
... Thanks Rory, I missed that requirement. Works perfectly now! Ravi On Jun 10, 2014, at 9:51 AM, Rory Stark wrote: > Hi Ravi- > > It looks like your sample sheet is missing the "bamReads" column, which > tells DiffBind where the bam files are that contain the aligned reads, so > dba. ...
written 5.0 years ago by Ravi Karra140
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dba.counts error
... Hi, I am trying to use DiffBind to analyze my ChIP-Seq data. I used MACS2 as my peak caller and to adjust for input. I am able to use dba to load in the data and to generate a correlation heatmap using the MACS scores. However, I am unable to calculate a binding matrix based on affinity scores. ...
diffbind written 5.0 years ago by Ravi Karra140 • updated 5.0 years ago by Rory Stark2.8k
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goseq/nullp with non-native identifiers
... Hello, I am trying to use goseq to find enriched GO terms for zebrafish RNA- seq data and am looking for advice on manually providing gene length information and GO annotation to goseq. My RNA-Seq data is mapped to danRer7 Ensembl gene id's. Unfortunately danRer7 does not appear to be supporte ...
annotation go zebrafish goseq written 6.7 years ago by Ravi Karra140 • updated 6.7 years ago by Alicia Oshlack100
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What populates makeTranscriptDbFromBiomart?
... Hi, Just starting to learn how to look at RNA Seq data, so apologies in advance. I ran my RNA-Seq experiment on a GAII and aligned to the zebrafish genome using Bowtie2/Tophat2. I downloaded the current zebrafish genome (Zv9) and transcript gtf file from Ensembl for the reference indices. I am ...
edger written 7.1 years ago by Ravi Karra140 • updated 7.1 years ago by Steve Lianoglou12k
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Conversion of pfm to pwm using PWM()
... Hi, I am trying to find TF binding sites in a set of promoters using position frequency matrices (pfm's) from jaspar and transfac. I have gotten this to work before on my machine at home, but cannot seem to get this to run on campus. I am not sure why I get the following error as I thought PWM can ...
written 8.0 years ago by Ravi Karra140 • updated 8.0 years ago by Steve Lianoglou12k
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RMAPPER and whole genome TFBS information
... Hello, I am trying to identify all putative GATA binding sites in the mouse genome. Ideally, I want to get genomic coordinates for each "binding site" to enter into a GenomicRanges object (I know there will be a lot of hits) and to overlay this information with the results of a ChIP- Seq experimen ...
rmapper genomicranges written 8.1 years ago by Ravi Karra140 • updated 8.1 years ago by Vincent J. Carey, Jr.6.3k
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Comment: C: Mapping microarray probes to the genome using findOverlaps
... Thanks for the suppprt Herve! Do you or Benilton (or anyone else!) have any ideas on how to redesign the .ndf file to allow PdInfoBuilder to use the updated probeset information from these alignments? Thanks again for all of the help, Ravi On Mar 8, 2011, at 8:29 PM, Hervé Pagès wrote: > Hi Rav ...
written 8.2 years ago by Ravi Karra140
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Comment: C: Mapping microarray probes to the genome using findOverlaps
... Hi Benilton, I am pretty sure the rows are unique in my new ndf file (see below). However, how does pdinfobuilder determine uniqueness? While each row is unique, there is no column that has strictly unique elements... see for example PROBE_DESIGN_ID. Could that be the issue? As a somewhat relate ...
written 8.2 years ago by Ravi Karra140
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Comment: C: Mapping microarray probes to the genome using findOverlaps
... Hi Sean and Herve, Thanks a ton for the suggestions! I modified Herve's approach to use biomaRt. Zv9 is available via Biomart/Ensembl and has incorporated many of the VEGA transcripts, many of which are supposed to be on this array. I ended up mapping to the cdna's from zv9 and like Herve only ma ...
written 8.2 years ago by Ravi Karra140
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Comment: C: Mapping microarray probes to the genome using findOverlaps
... Hi Sean, I could do that, but am not sure how to. The annotated zebrafish genome is the Tubingen strain and the some of the probes on the array are from the EK and AB strains. This means that I need to allow for SNP's in the alignment. I originally tried to align the probes to the Ensembl Transc ...
written 8.2 years ago by Ravi Karra140

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Popular Question 5.0 years ago, created a question with more than 1,000 views. For goseq/nullp with non-native identifiers

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