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Forum: Bioinformatics 01-29-2013, 10:27 AM
Replies: 16
Views: 6,724
Posted By zlu
Hi Andreas, I've been getting result which...

Hi Andreas,

I've been getting result which is puzzling when doing a viral quasispecies analysis with LoFreq . When I ran lofreq_snpcaller.py with the -Q filter, I get less variants with the...
Forum: Bioinformatics 02-20-2012, 06:06 AM
Replies: 25
Views: 11,099
Posted By zlu
Hi, I'm trying to get hold of a copy of...

Hi,

I'm trying to get hold of a copy of MagicViewer but the download link at the site (http://bioinformatics.zj.cn/magicviewer/) is no longer valid. Is the program still available?
Forum: Bioinformatics 02-02-2012, 07:31 AM
Replies: 123
Views: 42,119
Posted By zlu
Smile That's what I thought. Thanks for the...

That's what I thought. Thanks for the clarification.

By the way, does anyone know of a "simple window-based" program (for the lab people :)) that is capable of calculating the consensus from a...
Forum: Bioinformatics 02-02-2012, 07:12 AM
Replies: 123
Views: 42,119
Posted By zlu
When I select the copy-to-clipboard option, the...

When I select the copy-to-clipboard option, the sequence that gets copied is in fact the reference sequence. So is the consensus here not referring to the real consensus of the mapping? In the...
Forum: Bioinformatics 08-01-2011, 05:38 PM
Replies: 8
Views: 2,909
Posted By zlu
Hi Brugger, do you mind sharing your solution?...

Hi Brugger, do you mind sharing your solution? Does this still involve recalibration using GATK? Thanks.
Forum: Bioinformatics 01-24-2011, 10:07 AM
Replies: 26
Views: 14,517
Posted By zlu
Before trying FREEC, I have a question which may...

Before trying FREEC, I have a question which may have a very simple answer. If I have a diploid organism and FREEC predicts the sample to have a gain of 6 copies; am I right to say that there are 3...
Forum: Bioinformatics 09-10-2010, 02:20 AM
Replies: 4
Views: 5,838
Posted By zlu
I'm trying to use CNV-seq on the bam files I...

I'm trying to use CNV-seq on the bam files I created with BWA and this may be really obvious but how do you decide which is ref and which is test. If I have 2 bam files generated by mapping Illumina...
Forum: Literature Watch 09-09-2010, 10:39 AM
Replies: 46
Views: 37,924
Posted By zlu
This may be really obvious but I'm trying to...

This may be really obvious but I'm trying to understand how to you decide which is ref and which is test. If I have 2 bam files generated by mapping Illumina reads from 2 individuals against the NCBI...
Forum: Bioinformatics 08-14-2010, 06:10 AM
Replies: 5
Views: 2,851
Posted By zlu
Rosyme, Thanks for suggesting the HikbertVis...

Rosyme, Thanks for suggesting the HikbertVis package. It seems to plot the coverage without any problem. However, do you know how to adjust the scale on the y-axis? I have some exceptionally high...
Forum: Bioinformatics 08-12-2010, 08:09 AM
Replies: 5
Views: 2,851
Posted By zlu
overlaying coverage plots

I'm trying to overlay coverage plots of individual chromosomes from different experiments to get a quick overview of probable CNVs. I've tried using simple xy plot, ggplot and plotrix packages of R...
Forum: Bioinformatics 07-12-2010, 07:00 AM
Replies: 366
Views: 181,413
Posted By zlu
Yes, I did: $ fastx_quality_stats -Q 33 -i...

Yes, I did:

$ fastx_quality_stats -Q 33 -i s_5_1_BC1_36bp_q5.fq -o s_5_1_BC1_36bp_q5.qualstats &
Forum: Bioinformatics 07-12-2010, 06:54 AM
Replies: 366
Views: 181,413
Posted By zlu
Using the fastqc and fastx_toolkit checking on my...

Using the fastqc and fastx_toolkit checking on my same set of sanger fastq file, the per base quality plots (attached) seems to give different result. I know that the boxplots from the 2 programs...
Forum: Bioinformatics 12-22-2009, 02:42 AM
Replies: 18
Views: 11,607
Posted By zlu
Using the patched emboss, I can now convert the...

Using the patched emboss, I can now convert the line wrapped fastq files. Thank you.
Forum: Bioinformatics 12-18-2009, 07:08 AM
Replies: 18
Views: 11,607
Posted By zlu
I'll try to patch it and see how it goes. ...

I'll try to patch it and see how it goes.



The compressed file is more than 1.3GB.

Thanks for your help. I'll try to process the fastq with a script.
Forum: Bioinformatics 12-18-2009, 05:56 AM
Replies: 18
Views: 11,607
Posted By zlu
yes, the lines are indedd wrapped. Thanks for the...

yes, the lines are indedd wrapped. Thanks for the reminder.

However, trying seqret of EMBOSS 6.1, I got the following error:

[SBSUser@pipeline Assembly2]$ seqret -sformat fastq-sanger
Reads...
Forum: Bioinformatics 12-18-2009, 03:05 AM
Replies: 18
Views: 11,607
Posted By zlu
Perhaps I didn't explain it clearly. I wasn't...

Perhaps I didn't explain it clearly. I wasn't trying to convert the Illumina short reads but mapped consensus sequence of a few chromosomes. Each is a few Mbp long, e.g:

@chr1...
Forum: Bioinformatics 12-17-2009, 10:06 AM
Replies: 18
Views: 11,607
Posted By zlu
converting consensus fastq to fasta

I was trying to convert fastq consensus sequneces (generated by the pileup2fq utility of samtools) to a multi-fasta file with the MAQ's fq_all2std.pl fq2fa script but it didn't work. The result is a...
Forum: Bioinformatics 12-15-2009, 03:25 AM
Replies: 18
Views: 8,805
Posted By zlu
My problem was actually due to the uneven number...

My problem was actually due to the uneven number of pair reads in the input fastq files. I was doing some quality filterings, mainly artefacts removal, on read1 and read2 separately and this resulted...
Forum: Bioinformatics 11-24-2009, 10:43 AM
Replies: 292
Views: 151,522
Posted By zlu
I'm wondering for a genome assembly project, will...

I'm wondering for a genome assembly project, will duplicate removal (with samtolls rmdup) and flitering out low mapping quality (e.g mapQ <10) improve my assembly? What do people usually do after...
Forum: Bioinformatics 11-18-2009, 07:40 AM
Replies: 292
Views: 151,522
Posted By zlu
Heng, This was done with BWA 0.5.4. For...

Heng,

This was done with BWA 0.5.4.

For resequencing project, does it really matter if the mates are not properly mapped? Can I instead just filter out those reads with low mapping qualities?
...
Forum: Bioinformatics 11-18-2009, 07:32 AM
Replies: 292
Views: 151,522
Posted By zlu
properly mapped Flag

Perhaps I have misunderstood it but isn't right that properly mapped flag (P string) are only used when read pairs are mapped to the same chromosome with correct insert size? I have about 6% of the...
Forum: Bioinformatics 11-13-2009, 10:32 AM
Replies: 292
Views: 151,522
Posted By zlu
But I'm using BWA. Is there an unmapped flag in...

But I'm using BWA. Is there an unmapped flag in the sam file?
Forum: Bioinformatics 11-13-2009, 10:22 AM
Replies: 292
Views: 151,522
Posted By zlu
Has anyone had any luck with this? In addition,...

Has anyone had any luck with this? In addition, in MAQ, you can dump unmapped reads into a separate file, is there such a function/tool in samtools? Thank you.
Forum: Bioinformatics 10-27-2009, 07:35 AM
Replies: 0
Views: 1,721
Posted By zlu
bwa sampe max insert size

Dear BWA users,

Checking through the sam file produced from the following commands:

bwa sampe -a 2792 ref.fa read1.sai read2.sai read1.fq read2.fq > read.pe.bwa.sam

I have found a high...
Forum: Bioinformatics 10-26-2009, 10:55 AM
Replies: 10
Views: 3,009
Posted By zlu
Our system is fairly similar: Linux pipeline...

Our system is fairly similar:

Linux pipeline 2.6.18-128.el5_BITS_XFS #1 SMP Thu Sep 3 17:05:45 BST 2009 x86_64 x86_64 x86_64 GNU/Linux

16 cores Intel(R) Xeon(R) CPU X7350 @ 2.93GHz

32GB...
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