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Forum: Bioinformatics 12-15-2010, 10:21 AM
Replies: 3
Views: 2,718
Posted By juan
BWA 0.5.9rc1

Being the early adopter, I tried using the -r option in bwa sampe from the latest version of bwa. If I understand correctly, this option will add the specified @RG tag to the SAM output file.
Has...
Forum: Illumina/Solexa 12-01-2010, 05:34 PM
Replies: 17
Views: 7,033
Posted By juan
200 million reads per lane? Is that the standard...

200 million reads per lane? Is that the standard or are you pushing the limit? What is the standard # of reads/lane for a HiSeq?
Is the RTA of the HiSeq the same as GAII? In a GAII run the...
Forum: Illumina/Solexa 10-27-2010, 06:56 PM
Replies: 0
Views: 2,272
Posted By juan
Red face Paired end reads: line # does not match

Hello,
I have a GAII paired-end run (seven lanes, run1 and run2 for each lane are the forward and reverse ends of a pair).

For 3 of the lanes, very few of the reads mapped successfully (< 20%). I...
Forum: Bioinformatics 09-22-2010, 06:31 AM
Replies: 24
Views: 33,896
Posted By juan
[QUOTE=maubp;25709]Solexa's negative quality...

[QUOTE=maubp;25709]Solexa's negative quality scores only went down to -5, so something else is going on.

I figured it out. 10 is the ASCII code for newline. bug in code not bizarre quality score.
Forum: Bioinformatics 09-21-2010, 01:25 PM
Replies: 24
Views: 33,896
Posted By juan
Quality score of -54(10)

Before mapping and before subtracting 64, I checked the distribution of quality scores for my reads (PIPELINE 1.6). I noticed what everyone mentioned here (quality scores starting at 66 - 64 = 2).
...
Forum: Bioinformatics 05-18-2010, 12:50 PM
Replies: 5
Views: 6,500
Posted By juan
Yes that is the problem with SAMtools. The...

Yes that is the problem with SAMtools. The majority of variants are in the 2nd half of the read, hence you have lots of false positives.
Forum: Bioinformatics 12-15-2009, 11:37 AM
Replies: 292
Views: 159,932
Posted By juan
I am also having this problem on linux. Did you...

I am also having this problem on linux. Did you find a solution?
Forum: SOLiD 12-04-2009, 05:00 PM
Replies: 67
Views: 195,185
Posted By juan
When converting from colorspace to basespace, if...

When converting from colorspace to basespace, if you reach an error (no color, aka "4" or "."), you have 4 possibilities for the rest of the read. How do you determine the correct one?

Example:...
Forum: SOLiD 10-29-2009, 09:13 AM
Replies: 15
Views: 10,734
Posted By juan
That's strange, the space between the 1 and the 3...

That's strange, the space between the 1 and the 3 at the end of the line is a bug in the FORUM code! When I tried to remove the space by clicking "edit", the space does not appear. It pops up during...
Forum: SOLiD 10-28-2009, 10:02 AM
Replies: 15
Views: 10,734
Posted By juan
should be? @226_3_65 ...

should be?
@226_3_65
T44411443424410204241340414444044433244322412334413
+
!!!51!!,!*!!4405!,!)'!2!)!!!!)!!!'5$!!0),!2(*5!!%+
Forum: SOLiD 10-28-2009, 10:00 AM
Replies: 15
Views: 10,734
Posted By juan
A question about the BFAST solid2fastq script: ...

A question about the BFAST solid2fastq script:
The SOLiD reads I have use "." instead of "4" for "N" basecalls. These bases have a qual score of -1.
After running the script on my reads, all the...
Forum: SOLiD 10-21-2009, 04:53 PM
Replies: 4
Views: 6,484
Posted By juan
If you convert from colorspace to [ATGC], how do...

If you convert from colorspace to [ATGC], how do you convert the QV value? Take the average?
Forum: Bioinformatics 09-11-2009, 01:38 PM
Replies: 2
Views: 3,114
Posted By juan
L is the sum of bases for the gene, not the exon,...

L is the sum of bases for the gene, not the exon, right?

RPKM does not account for splicing, nor does it distinguish between transcript isoforms.

I would include the intron in the L.
Forum: Bioinformatics 09-09-2009, 08:56 AM
Replies: 514
Views: 223,099
Posted By juan
Split Read RNA-Seq mapping with bowtie?

How does Bowtie handle RNA-seq data, has anyone tried? Can it map split reads? Any plans to add split-read mapping functionality?
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