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Search: Posts Made By: Alex Lee
Forum: Bioinformatics 12-11-2018, 05:18 AM
Replies: 1
Views: 1,738
Posted By Alex Lee
Post BAM -> FASTQ why can I not produce the same result?

Dear all, I've been trying to test if I can produce the same fusion call starting from BAM instead of FASQ. My STAR command is as such.

STAR --genomeDir /index/hg38.p5/ \
--readFilesIn...
Forum: Bioinformatics 03-07-2018, 02:35 PM
Replies: 244
Views: 107,320
Posted By Alex Lee
Hi Brian, I have a problem whereby I have a about...

Hi Brian, I have a problem whereby I have a about 12 fastq files and I'm not completely convinced that the barcode for each of the samples are as named in the key. If I have 12 unique 6-mer barcodes...
Forum: Bioinformatics 11-30-2015, 07:47 AM
Replies: 40
Views: 18,582
Posted By Alex Lee
Hi everyone, I was able to solve a similar...

Hi everyone, I was able to solve a similar problem to the original post, failed due to too many files open. This is my experience and some new stuff I learned.

1. My reads are about 40 GB per...
Forum: Bioinformatics 11-29-2015, 08:56 AM
Replies: 40
Views: 18,582
Posted By Alex Lee
Arun, thanks for the clarification and example. ...

Arun, thanks for the clarification and example. Just in case someone else might find this useful, I also found that a symbolic link works once the blastdb is prep. This way I just download it...
Forum: Bioinformatics 11-25-2015, 04:12 PM
Replies: 40
Views: 18,582
Posted By Alex Lee
Hi, so I actually got fusion, however, I still...

Hi, so I actually got fusion, however, I still confused about the blast database, from the instruction it wants a ./blast_human directory containing

human_genomic* and nt*

What does the...
Forum: Bioinformatics 08-30-2014, 08:27 PM
Replies: 3
Views: 6,032
Posted By Alex Lee
wow thanks Brian - bbmerge is more than that. ...

wow thanks Brian - bbmerge is more than that. Sorry for my mistake what I meant was to calculate "Mean Inner Distance between Mate Pairs". A benefit right of is that I see that its written in JAVA...
Forum: Bioinformatics 08-30-2014, 04:59 PM
Replies: 3
Views: 6,032
Posted By Alex Lee
Talking Estimating Paired insert size with Picard

HI all, I have paired reads, for & rev of 150 bp.
I used the picard tools to estimate insert size.
The output file has median size for both for & reverse with different sizes,
...
Forum: Bioinformatics 08-26-2014, 04:04 PM
Replies: 0
Views: 1,216
Posted By Alex Lee
BLAT settings to match is continuously on reference?

HI I have 100 bp sequences I would like to match against a reference region. Is there a way I can set BLAT so that the match (eg 80%) is continuous? For example what I don't want is for the the...
Forum: RNA Sequencing 07-07-2014, 01:43 PM
Replies: 1
Views: 1,746
Posted By Alex Lee
Smile Kmer changes after Trimming

Hi All,
I'm getting higher Kmers on my 5' end after trimming with trimmomatic-0.32. My samples are paired RNA-Seq from Illumina Miseq. I'm using FastQC Report to detect overrepresentation of...
Forum: RNA Sequencing 04-17-2014, 10:28 PM
Replies: 0
Views: 1,296
Posted By Alex Lee
Talking 3' trimming using cutadapt changes property of 5'.

Hi all,
beginner question here: I have an attached PDF before and after illustration.

I'm using the Galaxy suite and cutadapt on a single read, not paired. When I first run the fastqc report,...
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