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Search: Posts Made By: hari_iyer16
Forum: Bioinformatics 02-28-2014, 10:47 AM
Replies: 2
Views: 1,432
Posted By hari_iyer16
Thanks Devon. Will look into pysam.

Thanks Devon.
Will look into pysam.
Forum: Bioinformatics 02-28-2014, 08:55 AM
Replies: 1
Views: 974
Posted By hari_iyer16
Have you tried biomaRt package in R? Have found...

Have you tried biomaRt package in R? Have found it very useful for such purposes.
I think you might be able to use their site by uploading your file and foramtiing accordingly as the BED file.
Forum: Bioinformatics 02-28-2014, 08:51 AM
Replies: 2
Views: 1,432
Posted By hari_iyer16
Filter reads by mappability, unique reads, not more than 1 mismatches

Hi all,
I am working with ChIP-seq data and want to filter the reads with the following criteria: (A) mappable reads; (B) unique alignments (most likely based on MAPQ score) and (C) not more than 1...
Forum: Bioinformatics 04-12-2013, 12:46 PM
Replies: 3
Views: 1,269
Posted By hari_iyer16
pipe two inputs to a command (coverageBed)

Hi,
I am trying to run coverageBed on my data. Since it is huge, I have to split the data into each chromosome and run them separately. coverageBed takes two input files, the data.bed file...
Forum: Bioinformatics 04-11-2013, 06:12 PM
Replies: 4
Views: 2,479
Posted By hari_iyer16
The chip.bed is 4.8G, and the windows.bed...

The chip.bed is 4.8G, and the windows.bed (hg18_chromInfo.txt) is 352M.
I figured the error is due to memory problems, and based on a suggestion from another mailing group, I used the -counts option...
Forum: Bioinformatics 04-11-2013, 12:41 PM
Replies: 4
Views: 2,479
Posted By hari_iyer16
@GenoMax: Yes, it is in Bed format. In fact the...

@GenoMax: Yes, it is in Bed format. In fact the actual name used in the command is windows.bed. I changed the names while posting here to avoid cryptic names.

Here is the first few lines from the...
Forum: Bioinformatics 04-11-2013, 11:38 AM
Replies: 4
Views: 2,479
Posted By hari_iyer16
coverageBed error: terminate called after throwing an instance of 'std::bad_alloc'

Hi all,
I am trying to run coverageBed from Bedtools in a cluster.
I connected to the cluster using the following parameters:
qrsh -l mem_free=10G,h_vmem=12G,h_stack=256M

Following is the...
Forum: Bioinformatics 02-22-2013, 11:40 AM
Replies: 0
Views: 800
Posted By hari_iyer16
Using coverageBed in Galaxy

Hi, I am new to Galaxy. I want to compute the sequencing tag coverage in defined intervals (like 0-99 bp, 100-199 bp, 200-299 bp ...) across all chromosomes from a ChIP-seq data, which is in the BED...
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