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Forum: RNA Sequencing 08-24-2016, 01:01 PM
Replies: 4
Views: 4,301
Posted By sulicon
I happened to meet exactly the same error this...

I happened to meet exactly the same error this morning. It turns out there is something "wrong" in the transcript to gene mapping (tx2gene). I am using GENCODE mouse v10 transcriptome and the tx2gene...
Forum: Bioinformatics 10-24-2014, 11:38 AM
Replies: 6
Views: 2,181
Posted By sulicon
Thank you GenoMax. I will trim the low quality...

Thank you GenoMax. I will trim the low quality bases as you suggested.
Forum: Bioinformatics 10-20-2014, 01:17 PM
Replies: 6
Views: 2,181
Posted By sulicon
We got the data from another group. There is no...

We got the data from another group. There is no barcodes used, I assume each sample was sequenced on one entire lane. (right?)

We have checked about 10 samples, two samples mentioned above have...
Forum: Bioinformatics 10-18-2014, 10:51 PM
Replies: 6
Views: 2,181
Posted By sulicon
Thank you Devon for the explanation and...

Thank you Devon for the explanation and suggestion.
Forum: Bioinformatics 10-18-2014, 01:21 AM
Replies: 6
Views: 2,181
Posted By sulicon
Weird results at the 51st nucleotide

Hi all,

We just got some bisulfite sequencing data from a set of patients. After running FastQC on a few samples, we observed an extremely low quality score at position #51, for two samples.
...
Forum: General 06-24-2014, 09:17 PM
Replies: 10
Views: 5,877
Posted By sulicon
Thanks for the suggestion. Will have a look at...

Thanks for the suggestion. Will have a look at Rapid Run :)
Forum: General 06-24-2014, 09:09 PM
Replies: 10
Views: 5,877
Posted By sulicon
thanks for the info!

thanks for the info!
Forum: General 06-23-2014, 04:30 PM
Replies: 10
Views: 5,877
Posted By sulicon
Thank you again. Sorry for possible confusion...

Thank you again. Sorry for possible confusion here: We are interested in both general promoter DNA methylation patterns and miRNA expression profiles in human samples, as many as possible. The major...
Forum: General 06-23-2014, 04:11 PM
Replies: 10
Views: 5,877
Posted By sulicon
Thank you Devon! I thought I could get the reads...

Thank you Devon! I thought I could get the reads from only miRNAs. And I misunderstood miSeq as an abbr of "miRNA Sequening"...
Forum: General 06-23-2014, 04:00 PM
Replies: 10
Views: 5,877
Posted By sulicon
Hi Devon, We are dealing with human samples....

Hi Devon,

We are dealing with human samples. I am not familiar with miSeq. Per my understanding, there are only ~1100 human miRNAs annotated in miRBase, so ~500K fragments per sample means ~500...
Forum: General 06-23-2014, 02:37 PM
Replies: 10
Views: 5,877
Posted By sulicon
Cost of RRBS and miRNA sequencing for ~50-100 samples?

Hi,

We are planning to measure the methylation and miRNA expression profiles for a set of samples (50-100). For methylation measurement, we just need to cover the promoter regions, so RRBS is...
Forum: General 08-12-2011, 02:21 PM
Replies: 3
Views: 2,345
Posted By sulicon
Question Cheapest solution for targeted sequencing?

Hi,

We have 500-1000 genomic DNA samples and we are interested in a set of ~20 loci. What's the most affordable way to sequence the 20 loci for all the samples?

Thanks,
Shuli
Forum: Bioinformatics 08-02-2011, 04:14 PM
Replies: 2
Views: 1,355
Posted By sulicon
Thanks, swbarnes2. These indels are called...

Thanks, swbarnes2.

These indels are called from the sequencing data of some clones. Each clone corresponds to one mRNA molecule and there is at most one clone for a locus in the library. What we...
Forum: Bioinformatics 08-02-2011, 02:03 PM
Replies: 2
Views: 1,355
Posted By sulicon
Can I always get the net gain/loss of nts from an indel?

Hi,

I'm analyzing SNPs and Indels called from alignments. I always observed indels described as in the following example:

chr6 111368147 . ATCT ATCTTCT 184 . ...
Forum: Bioinformatics 07-29-2011, 02:58 PM
Replies: 1
Views: 3,803
Posted By sulicon
Questions about generating consensus sequences from the VCF file

Hi all,

I'm trying to get the most reliable consensus sequence from raw VCF files generated by samtools and bcftools. I tried "vcfutils.pl" coming with samtools, but I always got warning messages...
Forum: Bioinformatics 07-27-2011, 12:22 PM
Replies: 3
Views: 4,578
Posted By sulicon
Thanks a lot :) The key is skipping double errors...

Thanks a lot :) The key is skipping double errors when the quality score is high enough, as you mentioned in your last sentence.
Forum: Bioinformatics 07-26-2011, 05:06 PM
Replies: 3
Views: 4,578
Posted By sulicon
Any suggestion for calculating overall Phred scale quality score for a sequence?

Hi all,
I have some consensus nucleotides and ptential variant sites with quality scores (phred scale) generated by mpileup and bcftools. We are working on some protein analysis, so I'm trying to...
Forum: Bioinformatics 06-08-2011, 10:13 PM
Replies: 3
Views: 2,178
Posted By sulicon
Thanks. It seems this package doesn't output the...

Thanks. It seems this package doesn't output the gap regions directly:

The genomic intervals between the "start" and "end" of the query that are "covered" by the alignment. Saying that the full...
Forum: Bioinformatics 06-06-2011, 12:14 PM
Replies: 3
Views: 2,178
Posted By sulicon
How to call "gaps" from spliced read alignment?

Hi all,

I have aligned my long 454 reads to the reference genome by using GMAP, a spliced read aligner. Now I want to extract the best set of intronic regions (gaps) in the alignments. Is there...
Forum: Bioinformatics 05-24-2011, 05:12 PM
Replies: 12
Views: 7,472
Posted By sulicon
It seems that "MapSplice" fits my needs very...

It seems that "MapSplice" fits my needs very well. It splits the raw reads into fragments first, so it could deal with both short and long reads.

http://www.netlab.uky.edu/p/bioinfo/MapSplice
Forum: Bioinformatics 05-24-2011, 02:28 PM
Replies: 12
Views: 7,472
Posted By sulicon
I have met the same problem. I have also had a...

I have met the same problem. I have also had a look at G-Mo.R-Se, a Tophat alternative. Again, the aligner it uses -- SOAP, only works with short reads...

Still looking for a splicing junction...
Forum: Bioinformatics 05-24-2011, 02:14 PM
Replies: 6
Views: 3,639
Posted By sulicon
Thanks Li Heng and Jose. I have tried GMAP and...

Thanks Li Heng and Jose. I have tried GMAP and checked the output. It looks good. According the a document I have found, GMAP outperforms BLAT for gene structure identification in both speed and...
Forum: Bioinformatics 05-18-2011, 01:43 PM
Replies: 6
Views: 3,639
Posted By sulicon
Spliced aligner for 454 reads?

Hi all,
I am trying to assemble 454 reads by aligning them to reference genome.

I have tried the official gsMapper before, which just gave me exon sequences, rather than transcripts sequences....
Forum: Bioinformatics 03-03-2011, 03:38 PM
Replies: 11
Views: 3,640
Posted By sulicon
It turns out that the reason for this is I've...

It turns out that the reason for this is I've forgot to 'export' the GOLDENPATH variable... Everything is OK now.
Forum: Bioinformatics 03-01-2011, 01:15 PM
Replies: 11
Views: 3,640
Posted By sulicon
I don't have this file. Is it required? And the...

I don't have this file. Is it required? And the problem is that even the reference genome can't be recognized:
"Error: Reference file/directory does not exist: hg19"

Maybe I need the "bigZips"...
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