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Search: Posts Made By: yueluo
Forum: Bioinformatics 10-08-2018, 12:14 AM
Replies: 14
Views: 4,604
Posted By yueluo
You don't need to run 'make install' for Trinity...

You don't need to run 'make install' for Trinity to work. Just execute /path/to/Trinity .
Forum: Bioinformatics 10-09-2016, 12:49 AM
Replies: 1
Views: 1,291
Posted By yueluo
Honestly, you might have better luck posting on...

Honestly, you might have better luck posting on GATK's forum.
Forum: Bioinformatics 03-13-2016, 09:31 PM
Replies: 3
Views: 3,030
Posted By yueluo
I had problems compiling bowtie2 with TBB support...

I had problems compiling bowtie2 with TBB support too. My OS was Centos 6.6. Bowtie2 source and TBB versions were the same as yours.
My 'fix' was to compile with LDFLAGS=-L/pathto/lib(or...
Forum: Bioinformatics 11-23-2015, 06:29 PM
Replies: 5
Views: 2,011
Posted By yueluo
Use the absolute path to your trinity program or...

Use the absolute path to your trinity program or add that directory to your system PATH.
Forum: Bioinformatics 11-18-2015, 01:42 AM
Replies: 1
Views: 2,211
Posted By yueluo
The 'I's you're seeing are quality scores of your...

The 'I's you're seeing are quality scores of your read, not the CIGAR string ...
'I' in phred-33 qual is 40. Where did you get the read file and how did you perform your alignment ? I think some...
Forum: Bioinformatics 11-04-2015, 11:58 PM
Replies: 9
Views: 3,536
Posted By yueluo
Try installing a newer version of samtools. ...

Try installing a newer version of samtools.

http://cole-trapnell-lab.github.io/cufflinks/getting_started/#installing-the-sam-tools
Forum: Bioinformatics 09-29-2015, 12:11 AM
Replies: 6
Views: 1,996
Posted By yueluo
That is not a valid fasta file. ...

That is not a valid fasta file.

https://en.wikipedia.org/wiki/FASTA_format
Forum: Bioinformatics 09-27-2015, 08:52 PM
Replies: 6
Views: 1,996
Posted By yueluo
Are you sure nothing was done the your sequences?...

Are you sure nothing was done the your sequences? 100% reads surviving does not necessarily mean no trimming was performed, especially when you don't specify MINLEN.
Forum: Bioinformatics 09-21-2015, 06:12 PM
Replies: 1
Views: 1,129
Posted By yueluo
You have inconsistent chromosome names - 1,2,3......

You have inconsistent chromosome names - 1,2,3... for your input vcf file and chr1,chr2,chr3... for your reference genome file.
An edit on either file should fix the problem.
Forum: Bioinformatics 07-02-2015, 08:25 PM
Replies: 15
Views: 6,052
Posted By yueluo
What files/directories do you have in your...

What files/directories do you have in your trimmomatic path? You might be missing some files.
Forum: Bioinformatics 04-24-2015, 03:32 AM
Replies: 5
Views: 2,604
Posted By yueluo
If you have a smaller fragment size than read...

If you have a smaller fragment size than read length, you will get adapter sequence on the 3' -end of your reads. I think you can try running Brians' bbmerge to merge reads by overlapping.
Forum: Bioinformatics 03-30-2015, 02:46 AM
Replies: 19
Views: 8,135
Posted By yueluo
Thanks for the input, so bowtie1 has the highest...

Thanks for the input, so bowtie1 has the highest mapping rate but also significantly high incorrect rate. Sound like a terrible tradeoff.
Forum: Bioinformatics 03-30-2015, 02:23 AM
Replies: 19
Views: 8,135
Posted By yueluo
For miRNA data, I would suggest using bowtie...

For miRNA data, I would suggest using bowtie instead of bowtie2, since the author claims bowtie to be more sensitive for reads <50bps.

Also, I would suggest you make a database from Rfam and...
Forum: RNA Sequencing 03-23-2015, 02:13 AM
Replies: 4
Views: 3,225
Posted By yueluo
As the Usage is trying to tell you... You need to...

As the Usage is trying to tell you... You need to add the following flags to your command:
--input=bam --output=bed
Also, convert2bed reads/writes through stdin and stdout, which in your case...
Forum: Bioinformatics 03-23-2015, 02:00 AM
Replies: 2
Views: 1,457
Posted By yueluo
Took a quick look at both Ensembl and Ncbi...

Took a quick look at both Ensembl and Ncbi considering the transcript "NM_001042565". I tried its gene "Wsb1" to get all the transcript information.

NM_001042565.3 = ENSMUST00000017821 (Wsb1-001)...
Forum: Bioinformatics 12-24-2014, 07:36 PM
Replies: 2
Views: 1,821
Posted By yueluo
3% variant frequency does not pass the default...

3% variant frequency does not pass the default minimum variant frequency for Varscan, which is 0.2(20%) for "mpileup2cns". You can change the threshold with '--min-var-freq' option.
Forum: Bioinformatics 12-17-2014, 07:35 PM
Replies: 36
Views: 18,914
Posted By yueluo
If you have a gtf/gff of the rRNA genes, you can...

If you have a gtf/gff of the rRNA genes, you can filter alignment results with Cufflinks using the '-M/--mask-file' option.

http://cole-trapnell-lab.github.io/cufflinks/cufflinks/index.html
Forum: Bioinformatics 09-24-2014, 09:59 PM
Replies: 4
Views: 1,243
Posted By yueluo
This looks like fasta to me, I'm still not sure...

This looks like fasta to me, I'm still not sure what "collapsed reads" mean.
You can add "-f" to your bowtie command for alignment of reads in fasta format.
Forum: Bioinformatics 07-24-2014, 06:08 PM
Replies: 3
Views: 1,685
Posted By yueluo
What's in your assemblies.txt file?? It...

What's in your assemblies.txt file??

It appears that cuffmerge is reading a GTF when it expects the list of bamfiles.
Forum: Bioinformatics 07-14-2014, 10:47 PM
Replies: 21
Views: 8,079
Posted By yueluo
Hi, have you tried running cuffdiff or cuffquant...

Hi, have you tried running cuffdiff or cuffquant with "accepted_hits.bam" files?

And how did you generate the "asd.bam" files anyway?
Forum: Bioinformatics 07-05-2014, 11:16 AM
Replies: 23
Views: 5,139
Posted By yueluo
You need the newest version of tophat ...

You need the newest version of tophat

http://ccb.jhu.edu/software/tophat/index.shtml
Forum: Bioinformatics 07-02-2014, 09:58 PM
Replies: 3
Views: 1,109
Posted By yueluo
The output files named "isoforms*" contain...

The output files named "isoforms*" contain information on transcript level.
Forum: Bioinformatics 06-24-2014, 03:41 AM
Replies: 11
Views: 3,996
Posted By yueluo
cuffcompare is not meant to calculate transcript...

cuffcompare is not meant to calculate transcript abundances, it is used to compare your assembled transcripts against the reference.
cuffcompare produces a new gtf, which you can use to run...
Forum: RNA Sequencing 06-23-2014, 07:04 PM
Replies: 7
Views: 3,948
Posted By yueluo
I usually remove reads that map to rRNA(and/or...

I usually remove reads that map to rRNA(and/or other sources of contamination) , then proceed with mapping/DE-analysis .
Forum: Bioinformatics 05-01-2014, 01:44 AM
Replies: 12
Views: 6,758
Posted By yueluo
Trinity’s In silico Read Normalization can handle...

Trinity’s In silico Read Normalization can handle paired reads.
Showing results 1 to 25 of 82

 


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