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Forum: Bioinformatics 07-09-2015, 04:39 AM
Replies: 1
Views: 1,516
Posted By swaraj
The output of StringTie should be in GTF format...

The output of StringTie should be in GTF format which reports Exons. The 9th column of the output contains name of transcript for each exon. If you visualise the GTF in IGV or some other genome...
Forum: RNA Sequencing 02-24-2015, 05:36 AM
Replies: 1
Views: 1,124
Posted By swaraj
This issue is discussed in a publication...

This issue is discussed in a publication (http://www.biomedcentral.com/1471-2164/12/516), which reports that accepting multi mapping reads (up to 10) is beneficial (Fig 1). It accounts for maximum...
Forum: Bioinformatics 02-23-2015, 06:32 AM
Replies: 0
Views: 1,230
Posted By swaraj
Annocript: Annotation pipeline for coding and long non-coding RNAs

Dear All,

We have developed a pipeline to annotate coding and long non-coding RNAs in transcriptome datasets. The pipeline is unix based and requires a multi-FASTA file of transcripts...
Forum: Bioinformatics 10-21-2013, 09:09 AM
Replies: 2
Views: 2,231
Posted By swaraj
Hey Obifro, Cool job!!! I was about to code...

Hey Obifro,

Cool job!!! I was about to code for a script when I came across your post. It saved me some time. Thanks.
Forum: Bioinformatics 09-24-2013, 05:56 AM
Replies: 8
Views: 3,502
Posted By swaraj
In step 2 I coverted transcript BED file into...

In step 2 I coverted transcript BED file into exon file. Here the name of each exon is the transcript name which means transcript name is reduddant. In step 5 this same file is converted back into...
Forum: Bioinformatics 09-23-2013, 07:30 AM
Replies: 8
Views: 3,502
Posted By swaraj
Dear Jason, A much quicker solution is to ...

Dear Jason,

A much quicker solution is to

1. Convert GTF to BED. A nice script is found here http://ea-utils.googlecode.com/svn/trunk/clipper/gtf2bed

2. Convert the BED file to exon...
Forum: Bioinformatics 06-27-2013, 07:24 AM
Replies: 1
Views: 618
Posted By swaraj
This should help. ...

This should help.

http://www.ncbi.nlm.nih.gov/pubmed/21897427
Forum: Bioinformatics 06-27-2013, 06:22 AM
Replies: 1
Views: 1,501
Posted By swaraj
If you have a reference trasncriptome to use...

If you have a reference trasncriptome to use while mapping with Tophat, then I suggest to leave -g to its default value and use --prefilter-multihits. This takes care of many of the multiple...
Forum: Bioinformatics 06-20-2013, 07:10 AM
Replies: 0
Views: 801
Posted By swaraj
Cufflinks: Missing assembly of reads

I am working on the zebrafish genome. I took out two regions of the genome hence called good and tricky

good: chr1 44689765 44728408
tricky: chr1 44619749 44656560

From my BAM file, reads...
Forum: Bioinformatics 06-19-2013, 10:48 AM
Replies: 0
Views: 958
Posted By swaraj
Cufflinks missing transcript assembly in random genomic loci

Dear All,

I am running Cufflinks on RNAseq data from 2 samples. The parameters I have used for both the samples are

--frag-bias-correct --library-type fr-unstranded --upper-quartile-norm...
Forum: RNA Sequencing 05-24-2013, 06:20 AM
Replies: 2
Views: 2,687
Posted By swaraj
1. I have noticed that disabling the -M option...

1. I have noticed that disabling the -M option allows for more reads to map especially in repeat rich regions. I do not think -M is automatically enabled with -G, at least in tophat 2.0.8b which I am...
Forum: Bioinformatics 04-03-2013, 05:43 PM
Replies: 0
Views: 2,247
Posted By swaraj
RPKM threshold estimation

Dear All,

I have a doubt in the calculation of False postitive rate while checking for FPKM threshold in a RNAseq experiment.

Following the method previously published...
Forum: Bioinformatics 02-25-2013, 11:46 AM
Replies: 8
Views: 3,502
Posted By swaraj
Raw counts of 12 column bed file (against multiple BAM)

Hello Everyone,

I am sharing a perl script to get raw read counts from mulitple BAM files, for a given bed file. The script requires bedtools and samtools to be preinstalled in the system.

I...
Forum: Bioinformatics 10-15-2012, 02:28 AM
Replies: 21
Views: 32,407
Posted By swaraj
I have a question about cuffmerge and...

I have a question about cuffmerge and cuffcompare. I have three samples and have independently assembled each using cufflinks. I am only interested in intergenic long non-coding RNA transcripts.
...
Forum: RNA Sequencing 06-13-2012, 09:49 AM
Replies: 67
Views: 68,891
Posted By swaraj
I am afraid I cant help you with this. These...

I am afraid I cant help you with this. These options belong to the chipscan task of scripture, which I have not used before and the documentation does not tell about. I have relied previously on...
Forum: Bioinformatics 06-13-2012, 06:22 AM
Replies: 11
Views: 4,464
Posted By swaraj
Assuming you have linux 64 bit installed in your...

Assuming you have linux 64 bit installed in your computer.

1. Download http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred.

2. Convert a downlaoded gtf annotation file into...
Forum: RNA Sequencing 06-13-2012, 04:50 AM
Replies: 67
Views: 68,891
Posted By swaraj
A few points I would like to make. 1. I have...

A few points I would like to make.

1. I have tried both cufflinks and scripture to assemble transcripts from RNAseq data in Tetraodon. Cufflinks outperforms scripture in terms of the assembly...
Forum: Bioinformatics 05-01-2012, 03:06 AM
Replies: 11
Views: 3,315
Posted By swaraj
Try to use cuffcompare utility from the cufflinks...

Try to use cuffcompare utility from the cufflinks package to compare transcripts gtf file against a gtf of known proteins. The cuffcompare binary gives a tracking file as result which can be parsed...
Forum: RNA Sequencing 04-10-2012, 06:02 AM
Replies: 3
Views: 2,899
Posted By swaraj
This is abosolutely fantastic news, was looking...

This is abosolutely fantastic news, was looking forward to it for a long time!!!
Forum: Bioinformatics 04-03-2012, 06:58 AM
Replies: 19
Views: 10,761
Posted By swaraj
Samtools is a problem only if one has to use...

Samtools is a problem only if one has to use Scripture for downstream analysis. I would suggest though to go with picard tools once, and keep your fingers crossed :-).
Forum: Bioinformatics 04-03-2012, 04:06 AM
Replies: 2
Views: 914
Posted By swaraj
TO GET CLASSIFICATION OF MAPPED READS "samtools...

TO GET CLASSIFICATION OF MAPPED READS
"samtools view sorted.bam | awk '{print $2}' | sort | uniq -c"
#THIS GIVES A RESULT
83839545 0
83824316 16
6755765 256
6850132 272

HERE 0, 16, 256, 272...
Forum: RNA Sequencing 04-03-2012, 04:05 AM
Replies: 6
Views: 3,494
Posted By swaraj
I would ask you to include the genome in your...

I would ask you to include the genome in your tophat run

so you new command will be

"tophat -p 24 -G genes.gtf /path/to/genome -o K562_1 hg19 reads.fastq"

The genome file name would be the...
Forum: Bioinformatics 04-03-2012, 03:54 AM
Replies: 10
Views: 3,837
Posted By swaraj
At this point Biomart is the most comprehensive...

At this point Biomart is the most comprehensive service to download all non-coding data for multiple organisms. The non-coding RNA are classified into various sub.-categories which have to selected...
Forum: Bioinformatics 04-03-2012, 03:19 AM
Replies: 12
Views: 6,501
Posted By swaraj
I have found picard tools very useful for...

I have found picard tools very useful for generating post alignment statistics

1. Get read map statistics
java -Xmx10000m -jar picard-tools-1.58/BamIndexStats.jar I= sorted.bam >sorted.stats
...
Forum: Bioinformatics 04-03-2012, 03:06 AM
Replies: 10
Views: 3,475
Posted By swaraj
Fragment your gtf file into five separate chunks...

Fragment your gtf file into five separate chunks and run each with gffread. it may help you unserstand the core of the fault.
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