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Forum: Bioinformatics 10-27-2016, 04:51 PM
Replies: 1
Views: 5,692
Posted By jazz
SA tag in SAM file for chimeric reads

Hi,
I am using BWA-mem for split read alignment for my single end genomic DNA-seq from Illumina. I know that BWA uses SA tag for marking chimeric reads. When I manually BLAST individual reads with...
Forum: Illumina/Solexa 05-11-2015, 12:11 PM
Replies: 5
Views: 1,757
Posted By jazz
I am trying to prepare GRO-seq libraries and not...

I am trying to prepare GRO-seq libraries and not mRNA-seq. Hence, I need to use a home-brew method versus a commercial kit.
Forum: Illumina/Solexa 05-10-2015, 08:37 AM
Replies: 5
Views: 1,757
Posted By jazz
Just trying to bump this thread up. Anyone with...

Just trying to bump this thread up. Anyone with experience in making strand-specific RNAseq libraries using the cDNA circularization method or 2nd strand synthesis with dUTP incorporation.

Thanks!
Forum: Illumina/Solexa 04-28-2015, 08:15 AM
Replies: 5
Views: 1,757
Posted By jazz
cDNA circularization versus UDG based strand specific RNA-seq construction

I need to construct strand-specific RNA-seq libraries for a class of non-coding RNAs in my system and I am considering 2 alternative library construction methods for producing strand-specific reads...
Forum: Bioinformatics 03-30-2015, 07:44 AM
Replies: 4
Views: 4,421
Posted By jazz
Thanks. I will check the RUVseq. Can I use RPKM...

Thanks. I will check the RUVseq. Can I use RPKM for my case?
Forum: Bioinformatics 03-27-2015, 01:40 PM
Replies: 4
Views: 4,421
Posted By jazz
Normalize small RNA data with spike-in controls?

Dear all,

I am planning to sequence small RNAs from my control and mutant cells and I was wondering what is the best way to normalize the data. My initial data shows that the small RNAs in...
Forum: Bioinformatics 12-18-2014, 09:50 AM
Replies: 3
Views: 988
Posted By jazz
Thanks for the prompt reply bruce01, but I...

Thanks for the prompt reply bruce01, but I thought that bedtools will report all the common overlap features between my gff and bam/bed. I only need to extract the reads which are overlapping the...
Forum: Bioinformatics 12-18-2014, 07:20 AM
Replies: 3
Views: 988
Posted By jazz
Identify reads overlapping a junction in gff file

Dear all,

I have a gff annotation file with coordinates for an overlapping genomic feature, e.g.
chr1 1-100
chr1 100-250
chr1 250-300
chr1 300-500

and an alignment file (bam/bed) with reads...
Forum: Bioinformatics 07-26-2013, 09:04 AM
Replies: 0
Views: 1,159
Posted By jazz
Normalization for RNA-IP experiment

I have some Illumina sequencing reads from two RNA-IP experiments, one utilizing the test antibody and the other with a control antibody (IgG). I did a small scale sequencing and got 2 mill and...
Forum: Bioinformatics 07-10-2013, 05:17 AM
Replies: 4
Views: 3,563
Posted By jazz
But bowtie1 does not allow for gapped alignment...

But bowtie1 does not allow for gapped alignment and I am expecting some possible small RNAs coming from fusion/chimeras. I am thinking about Blat and Tophat fusion. Any suggestions on those?
Forum: Bioinformatics 07-09-2013, 03:22 PM
Replies: 4
Views: 3,563
Posted By jazz
Bowtie2 mismatches option for small RNA mapping

I am using Bowtie2 to map small RNA reads (not microRNAs) to the genome. To account for allelic divergence, I need to set it to allow 1 or maybe even 2 mismatches. Is it possible to change that? I...
Forum: Bioinformatics 07-01-2013, 09:04 AM
Replies: 8
Views: 3,064
Posted By jazz
I tried it again and this time it gave a sane...

I tried it again and this time it gave a sane output like this

scaffold68 3144 3165 JLK5VL1:383:H0TDTADXX:1:1116:17468:54631 42 +...
Forum: Bioinformatics 07-01-2013, 08:59 AM
Replies: 8
Views: 3,064
Posted By jazz
Sorry! Here is the command I tried: ...

Sorry!

Here is the command I tried:

intersectbed -a Inputfile.bed -b compare.gff > output.bed

The first few lines of the resulting bed file look like this:

BAM◊‹%@HD VN:1.0 SO:unsorted...
Forum: Bioinformatics 07-01-2013, 08:32 AM
Replies: 8
Views: 3,064
Posted By jazz
I am getting a bizarre result from using the...

I am getting a bizarre result from using the intersectbed from bedtools. The output bed file contains strange characters and not the chromosomal coordinates as I expected.
Any suggestions?
Can...
Forum: Bioinformatics 06-28-2013, 07:03 PM
Replies: 45
Views: 14,884
Posted By jazz
never mind, I solved it!

never mind, I solved it!
Forum: Bioinformatics 06-28-2013, 06:31 PM
Replies: 45
Views: 14,884
Posted By jazz
After a 'make check' I get the following error ...

After a 'make check' I get the following error

jkhurana@jkhurana-ThinkPad-T530:~/Downloads/libgtextutils-0.6.1$ make check
Making check in m4
make[1]: Entering directory...
Forum: Bioinformatics 06-28-2013, 06:27 PM
Replies: 45
Views: 14,884
Posted By jazz
libgtextutils installation problem for FASTX toolkit

I am trying to install libgtextutils for running the FASTX toolkit on my Ubuntu, but I am getting the following error after 'sudo make install' command

Making install in m4
make[1]: Entering...
Forum: Bioinformatics 06-26-2013, 07:26 AM
Replies: 8
Views: 3,064
Posted By jazz
compare genomic features from gff file to a SAM/BED file

I have an alignment from Bowtie2 for my RNA-IP and I want to compile a pie chart of % of reads mapping to different genomic features like exons, introns, UTR's etc. I am planning to compare my...
Forum: Bioinformatics 06-06-2013, 11:59 AM
Replies: 16
Views: 3,902
Posted By jazz
Thanks everyone. I will give these suggestions a...

Thanks everyone. I will give these suggestions a try and let you know how it went.
Forum: Bioinformatics 06-05-2013, 12:16 PM
Replies: 16
Views: 3,902
Posted By jazz
Split SAM/BAM files into thousands of contigs

Hi,

I am new to bioinformatics and programming, so this might be too easy to tackle for some of you. I am working on a newly sequenced genome with thousands of contigs. I have Illumina sequence...
Forum: Sample Prep / Library Generation 05-29-2013, 06:01 AM
Replies: 35
Views: 22,519
Posted By jazz
This is the problem with companies in general....

This is the problem with companies in general. They sell kits with 'proprietary' components and won't disclose any other information.
15' does sound insufficient but maybe they are using a modified...
Forum: Sample Prep / Library Generation 11-10-2011, 07:25 PM
Replies: 35
Views: 22,519
Posted By jazz
What are your thoughts about Superscript II? I...

What are your thoughts about Superscript II? I have seen a few protocols which use Superscript II for first strand synthesis and I think there might be some advantage to it while there is already an...
Forum: Sample Prep / Library Generation 11-09-2011, 12:51 PM
Replies: 35
Views: 22,519
Posted By jazz
While we are discussing the usability of...

While we are discussing the usability of different reagents in preparing libraries, can anyone help me with my issue with Ampure beads. I just ordered them and wanted to test them for size retention...
Forum: Sample Prep / Library Generation 11-02-2011, 09:51 AM
Replies: 35
Views: 22,519
Posted By jazz
Yes, I failed to mention that I needed to...

Yes, I failed to mention that I needed to multiplex my samples and have paired-end reads.
Forum: Sample Prep / Library Generation 11-02-2011, 09:43 AM
Replies: 35
Views: 22,519
Posted By jazz
Directional RNA-seq: Illumina Tru-seq versus dUTP based method

I guess the title says it all here. I am looking for an RNA-seq protocol which preserves strand-specificity, and came across this paper.

Comprehensive comparative analysis of strand-specific RNA...
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