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Search: Posts Made By: capricy
Forum: Bioinformatics 04-22-2018, 08:54 AM
Replies: 2
Views: 323
Posted By capricy
Surely, I do care about accuracy! Pilon used...

Surely, I do care about accuracy!

Pilon used bam files, which contains the information about the mapped reads. But the independent Illumina contigs contain much more information than that. That's...
Forum: Bioinformatics 04-22-2018, 04:12 AM
Replies: 2
Views: 323
Posted By capricy
tools for merging assembled genome

Hi, All,

I have two assembled genome files:

1. Illumina reads were subject to MIRA and the resultant assembly file is very fragmented.
2. PacBio reads were subjected to Canu and Quiver, and...
Forum: Bioinformatics 12-13-2017, 03:02 PM
Replies: 0
Views: 369
Posted By capricy
unexplained cuffdiff outputs for stranded libraries

Dear Community,

I recently had sequencing data from stranded library (second strand). The count output from STAR indicated that most of the reads mapped to the second strand. I then ran cuffdiff...
Forum: Bioinformatics 11-30-2017, 11:02 AM
Replies: 5
Views: 625
Posted By capricy
Thank you very much for advice about bringing...

Thank you very much for advice about bringing down the value for -p.

I will try that with larger memory.

Actually all my jobs are hanging at:

ChkbCpt1b
> Processing Locus...
Forum: Bioinformatics 11-29-2017, 02:47 AM
Replies: 5
Views: 625
Posted By capricy
Hi, Matt, Thank you very much for reply. ...

Hi, Matt,

Thank you very much for reply.

I am running on HPC. I used 96G mem, 40 processor. They are still running..., and last night I started to see the output for file: var_model.info

I...
Forum: Bioinformatics 11-28-2017, 03:35 AM
Replies: 5
Views: 625
Posted By capricy
speed up the cuffdiff calculation

Dear Community,

I have 12 sets of RNAseq data (4 groups) and mapped them using STAR. The resultant bam files ranged from 4G to 13 G. I then run cuffdiff on those bam files to get the FPKMs and...
Forum: Bioinformatics 06-07-2017, 04:54 PM
Replies: 0
Views: 349
Posted By capricy
RNAseq data for metabolic pathway reconstruction

Hello, there,

I wonder if anyone would recommend some metabolic pathway reconstruction tools? My data are mouse RNAseq data.

Thanks a lot!

C.
Forum: Bioinformatics 03-24-2017, 11:58 AM
Replies: 1
Views: 689
Posted By capricy
looking for a tools to predict peptide sequence from nucleotide sequence

Hello,

I have some assembled sequence with low coverage. Since the assembly quality is suboptimal, I am looking for a tool to predict the peptide sequence instead of directly translating.

I...
Forum: Bioinformatics 03-13-2017, 10:36 AM
Replies: 2
Views: 684
Posted By capricy
do you mean the first column? This indeed...

do you mean the first column?

This indeed is my first time to handle the .vcf file. But I did read the document and the all the examples I have found has number of chromosome instead of the...
Forum: Bioinformatics 03-13-2017, 09:11 AM
Replies: 2
Views: 684
Posted By capricy
snpeff : ERROR_CHROMOSOME_NOT_FOUND

Hello,

I got an issue with my bacterial snp annotation, that is, chromosome_not_found error. I did snp call using kSNP3.0.


Here are several lines of my vcf file:
====
##fileformat=VCFv4.0...
Forum: Illumina/Solexa 03-11-2017, 07:44 PM
Replies: 2
Views: 765
Posted By capricy
It is metagenomic data from fecal samples. I did...

It is metagenomic data from fecal samples. I did trim the samples with trimmomatic.
Forum: Illumina/Solexa 03-11-2017, 05:27 AM
Replies: 2
Views: 765
Posted By capricy
library insert size: too small

Hello,

I got some illumina data which obviously has very small insert size as many of the read pairs have >95% overlap. I went back to illumina library protocol and feel that it generally suggests...
Forum: Bioinformatics 02-04-2017, 08:56 PM
Replies: 0
Views: 525
Posted By capricy
cuffmerge:the same tss_id, but different leftmost exon

Hello, there,

I did de novo RNA-seq cufflinks assembly. I then merged transcripts.gtf files from different replicates to obtain merged.gtf in the absence of reference annotation.

This...
Forum: Bioinformatics 02-01-2017, 07:22 AM
Replies: 6
Views: 833
Posted By capricy
I didn't use -g since I only would like to see...

I didn't use -g since I only would like to see the de novo assembled transfrags.
Forum: Bioinformatics 02-01-2017, 07:10 AM
Replies: 6
Views: 833
Posted By capricy
According to the cuffcompare document, if I use...

According to the cuffcompare document, if I use -r <reference.gtf>, the output should be able to identify the overlapped transfrags. But it did not in my case.

Just wonder if there is something...
Forum: Bioinformatics 02-01-2017, 03:19 AM
Replies: 6
Views: 833
Posted By capricy
Then what is the easy way to annotate those...

Then what is the easy way to annotate those assembled transcripts? I meant, I would like to find the closest reference gene IDs for the transcripts.

Thanks.

C.
Forum: Bioinformatics 01-31-2017, 06:52 PM
Replies: 6
Views: 833
Posted By capricy
annotate cufflink assembled transcripts with reference gtf

Hello, there,

1. I did genome-guided de novo transcripts assembly for my RNAseq data using cufflinks. Here .sam file is from STAR mapping

cufflinks -p 8 /mapping/mapped.sam

2. I then merged...
Forum: Bioinformatics 01-19-2017, 03:26 PM
Replies: 1
Views: 869
Posted By capricy
SNP enrichment test along the genome

Hello, there,

I have SNP annotation along the genomic DNA. By visual inspection, I can tell that some chromosomal region tends to have more SNPs than the other. I wonder if there is a tool to...
Forum: Bioinformatics 01-16-2017, 01:18 AM
Replies: 2
Views: 1,952
Posted By capricy
Thank you so much for the information. I will...

Thank you so much for the information. I will explore those methods.

C.
Forum: Bioinformatics 01-14-2017, 06:28 AM
Replies: 4
Views: 1,946
Posted By capricy
The data were from E coli. New isolates. Library...

The data were from E coli. New isolates. Library is illumina miseq. Coverage was estimated from the assembly/reference alignment.
Forum: Bioinformatics 01-14-2017, 04:06 AM
Replies: 4
Views: 1,946
Posted By capricy
Hi, Daniel, I have similar question. My...

Hi, Daniel,

I have similar question. My illumina reads assembly covered about 50% of the genome. Do you have some updated ideas to share?

Thanks.

C
Forum: Bioinformatics 01-14-2017, 03:48 AM
Replies: 2
Views: 1,952
Posted By capricy
looking for reference-guided genome assembly tools

Hello, there,

I got the illumina data from two E coli isolate genomic DNA and try to do the assembly. There are many de novo assemblers around. I just wonder if there are any tools for...
Forum: Bioinformatics 06-02-2016, 07:31 AM
Replies: 0
Views: 487
Posted By capricy
about uniref database record

Hello, there,

The website mentions that subfragments with 11 or more residues are placed into a single record. My question is: how do I know whether or not a record is derived from merging the...
Forum: Bioinformatics 05-16-2016, 12:34 PM
Replies: 0
Views: 541
Posted By capricy
blastp error: Too many positional arguments (1), the offending value: std

Hello, there,

What I was trying to get is the format 6 standard output plus qlen. So, I am using the following command line:

/projects01/tools/ncbi-blast-2.2.28+/bin/blastp -outfmt "6 std qlen"...
Forum: Bioinformatics 01-04-2016, 05:47 PM
Replies: 1
Views: 651
Posted By capricy
confused by bowtie2 alignment score

Hello, there,

I am using default mode for bowtie2 reporting and the manual has it "Bowtie 2 does not garantee that the alignment reported is the best possible in terms of alignment score"


The...
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