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Search: Posts Made By: graceqy
Forum: Bioinformatics 10-25-2016, 09:48 AM
Replies: 2
Views: 3,051
Posted By graceqy
The Phylip developed solved the puzzle - the...

The Phylip developed solved the puzzle - the names are too short.
Forum: Bioinformatics 10-24-2016, 02:59 PM
Replies: 2
Views: 3,051
Posted By graceqy
Unexpected end-of-file ERR with PHYLIP

I was testing Phylip protdist using the default setting. My input file is:

7 9
4950 CTREGLTAS
4376 CARWETGTA
4752 CARELTGTT
5657 CARSGNGST
4348 CAR-GVSSA
1548 CARSDLGPA
4451 ...
Forum: Bioinformatics 10-19-2016, 05:45 AM
Replies: 2
Views: 1,456
Posted By graceqy
Got it. Thanks!

Got it. Thanks!
Forum: Bioinformatics 10-14-2016, 01:47 PM
Replies: 2
Views: 1,456
Posted By graceqy
Kallisto with refseq fasta file

Has anyone ever tried to use refseq instead of ensembl transcriptome fasta files for RNAseq analysis with Kallisto, pls? Would there be any concern for me to do so?
Forum: Bioinformatics 05-26-2016, 12:26 PM
Replies: 3
Views: 1,039
Posted By graceqy
I have tens of thousands of sequences. I need a...

I have tens of thousands of sequences. I need a similarity calculation that put sequences with > 70% similar to the same cluster.I don't think sort does that.
Forum: Bioinformatics 05-26-2016, 11:11 AM
Replies: 3
Views: 1,039
Posted By graceqy
Clustering very short sequences

Does anyone know any program that does clustering efficiently with super short sequences such as 3-4 amino acid long?

I was trying to cluster amino acid sequences by similarity and would like to...
Forum: Bioinformatics 10-21-2015, 03:00 PM
Replies: 2
Views: 2,348
Posted By graceqy
This really helps. Thank you very much!

This really helps. Thank you very much!
Forum: Bioinformatics 10-21-2015, 02:08 PM
Replies: 2
Views: 2,348
Posted By graceqy
Question on duplicate removal with STAR

I was trying to do duplicate removal after alignment with STAR, and here is how i ran the command line:

$ STAR --runMode inputAlignmentsFromBAM --inputBAMfile /dir/ti/my.sorted.bam...
Forum: Bioinformatics 10-07-2015, 03:05 PM
Replies: 2
Views: 2,614
Posted By graceqy
Sorry I figured it out. But I don't know how to...

Sorry I figured it out. But I don't know how to delete the post.
Forum: Bioinformatics 10-07-2015, 02:43 PM
Replies: 2
Views: 2,614
Posted By graceqy
STAR alignment with multiple fq files

I am trying to do RNAseq PE alignment using STAR. It works for one pair of fq files:

$ STAR --runThreadN 30 --genomeDir /srv/STAR_genome/human/ --readFilesIn /../RNA4_1_R1.fastq.gz...
Forum: Bioinformatics 10-07-2015, 02:07 PM
Replies: 6
Views: 2,189
Posted By graceqy
Thanks. By 30K vs 60K difference I meant...

Thanks.

By 30K vs 60K difference I meant the row numbers in the cufflinks output with the two different gtf files. The row numbers and genes are fixed for each regardless of the input bam files....
Forum: Bioinformatics 10-07-2015, 12:03 PM
Replies: 1
Views: 2,955
Posted By graceqy
FastQC in a pipeline

Hi,

We are running fastqc with the fq files before alignment with STAR. For now the fastqc output is a html file. I was wondering:

1. Could any of the output from fastqc be used to feed STAR...
Forum: Bioinformatics 10-07-2015, 11:10 AM
Replies: 6
Views: 2,189
Posted By graceqy
Thanks for the responses. I used...

Thanks for the responses.

I used GCA_000001405.15_GRCh38_no_alt_analysis_set.fna to build the genome for STAR. Does it mean gencode is the right gtf to use here?

Is it right that if I want to...
Forum: Bioinformatics 10-07-2015, 08:26 AM
Replies: 6
Views: 2,189
Posted By graceqy
Annotation difference between refSeq and Gencode

Hi all,

I am trying to set up an RNAseq work flow:

1. Generated genome files for STAR using .fna files from NCBI ftp and gtf files from Gencode;

2. Aligned fq using STAR, convert sam to...
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