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Search: Posts Made By: lh3
Forum: Bioinformatics 02-05-2015, 06:48 AM
Replies: 4
Views: 981
Posted By lh3
Don't touch the @SQ lines unless you thoroughly...

Don't touch the @SQ lines unless you thoroughly understand the BAM structure.
Forum: Bioinformatics 01-02-2015, 07:27 AM
Replies: 3
Views: 1,806
Posted By lh3
I put the mdust source code here: ...

I put the mdust source code here:

https://github.com/lh3/mdust
Forum: Bioinformatics 12-13-2014, 02:37 PM
Replies: 7
Views: 1,297
Posted By lh3
Option -H has no effect with -b, and a mapped BAM...

Option -H has no effect with -b, and a mapped BAM file always has @SQ lines. There is no way to strip them off. Please attach a SAM example if you believe samtools is wrong.
Forum: Bioinformatics 12-12-2014, 06:28 AM
Replies: 13
Views: 2,502
Posted By lh3
The end problem was first mentioned in a 2008...

The end problem was first mentioned in a 2008 paper and then rediscovered multiple times after that. The problem subsequently motivated the development of GATK realignment, SRMA, samtools BAQ and...
Forum: Bioinformatics 12-09-2014, 06:19 PM
Replies: 11
Views: 2,119
Posted By lh3
A sorted BAM is sometimes smaller than the gzip'd...

A sorted BAM is sometimes smaller than the gzip'd fastq (depending on coverage), but the unsorted BAM is larger most of time. Some bioinfo cores prefer BAM because BAM keeps meta information, such as...
Forum: Bioinformatics 12-07-2014, 09:49 AM
Replies: 10
Views: 9,341
Posted By lh3
Nice tips. Thanks!

Nice tips. Thanks!
Forum: Bioinformatics 12-06-2014, 09:00 AM
Replies: 4
Views: 1,606
Posted By lh3
bwa does not work with human data on 32-bit...

bwa does not work with human data on 32-bit machines.
Forum: Bioinformatics 11-25-2014, 06:20 PM
Replies: 1
Views: 1,437
Posted By lh3
Quite neat. Thanks.

Quite neat. Thanks.
Forum: Bioinformatics 10-28-2014, 04:58 AM
Replies: 7
Views: 1,017
Posted By lh3
If a sequence is present in both hg19 and GRCh37...

If a sequence is present in both hg19 and GRCh37 (and all its patches), they have exactly the same length and coordinate. The actual sequence may be different as ucsc converted all ambiguous bases to...
Forum: RNA Sequencing 10-27-2014, 05:01 AM
Replies: 6
Views: 2,091
Posted By lh3
*_random sequences could be unique sequences in...

*_random sequences could be unique sequences in heterochromatin or a large segdup where the flanking cannot be localized or placed. We use these sequences in mapping to reduce mapping artifacts, not...
Forum: Bioinformatics 10-21-2014, 06:17 PM
Replies: 10
Views: 9,341
Posted By lh3
I don't know how, but there must be ways with...

I don't know how, but there must be ways with their APIs.
Forum: General 10-21-2014, 06:14 PM
Replies: 9
Views: 1,597
Posted By lh3
I guess finding structural variations should be...

I guess finding structural variations should be easier with WGS due to even coverage.
Forum: Bioinformatics 10-21-2014, 05:02 PM
Replies: 10
Views: 9,341
Posted By lh3
See...

See https://gist.github.com/lh3/54f535b11a9ee5d3be8e
Forum: Bioinformatics 10-15-2014, 03:03 PM
Replies: 3
Views: 1,113
Posted By lh3
It should work, but will be very slow.

It should work, but will be very slow.
Forum: Bioinformatics 10-10-2014, 09:25 AM
Replies: 35
Views: 12,075
Posted By lh3
With the picard method, optical duplicates will...

With the picard method, optical duplicates will lead to an underestimate of the library size. The lower the coverage, the higher the bias. To see this, suppose we have 0.5% optical duplicate rate...
Forum: Bioinformatics 10-09-2014, 01:57 PM
Replies: 35
Views: 12,075
Posted By lh3
I see, it is conditioned. Then I understand why...

I see, it is conditioned. Then I understand why you say Picard's model is a special case of ZTNB.

Another question. Why did you say in bw's plot preseq cannot be compared to picard? Isn't preseq's...
Forum: Bioinformatics 10-09-2014, 11:03 AM
Replies: 35
Views: 12,075
Posted By lh3
Someone was asking me about library size...

Someone was asking me about library size estimate. Google search directed me to this interesting thread. I have a question about your ZTNB model.

I briefly skimmed through the supplementary note....
Forum: Bioinformatics 10-03-2014, 07:00 AM
Replies: 10
Views: 2,832
Posted By lh3
I forgot the version I was trying. It has been a...

I forgot the version I was trying. It has been a while. SNAP does require a lot of memory, tens of GB for human genome. I don't know if it works for genomes longer than 4GB.

I have talked to the...
Forum: Bioinformatics 10-02-2014, 07:27 PM
Replies: 10
Views: 2,832
Posted By lh3
My last comment was old. Recent snap is good. It...

My last comment was old. Recent snap is good. It is very fast and fairly accurate. What I am not sure is whether it is able to find a bit longer indels.
Forum: Bioinformatics 09-25-2014, 06:04 PM
Replies: 8
Views: 1,630
Posted By lh3
I overlooked it, too... An author told me the...

I overlooked it, too... An author told me the link yesterday.
Forum: Bioinformatics 09-25-2014, 12:27 PM
Replies: 8
Views: 1,630
Posted By lh3
PacBio assembly of CHM1 is here: ...

PacBio assembly of CHM1 is here:

http://www.cbcb.umd.edu/software/PBcR/MHAP/

It is different from the version I was looking at, but I believe it should be equally good. The NA12878 PacBio...
Forum: Bioinformatics 09-20-2014, 08:40 PM
Replies: 8
Views: 1,630
Posted By lh3
The best so far is the CHM1 pacbio assembly, but...

The best so far is the CHM1 pacbio assembly, but I don't if it has been publicly released yet. NA12878 also has pacbio assembly and public moleculo data (from 1000g ftp). These will be useful for...
Forum: Illumina/Solexa 09-11-2014, 06:23 PM
Replies: 1
Views: 873
Posted By lh3
This is a frequent issue around ployA.

This is a frequent issue around ployA.
Forum: Bioinformatics 09-11-2014, 06:19 PM
Replies: 9
Views: 4,923
Posted By lh3
For this particular read, the bwa-mem (0.7.10)...

For this particular read, the bwa-mem (0.7.10) alignment is:

1 0 1 25189065 60 57M44S
1 2048 2 169676055 60 51H50M

This is a chimeric...
Forum: Illumina/Solexa 09-05-2014, 07:01 AM
Replies: 25
Views: 3,953
Posted By lh3
As to cost, Illumina is advertising $1000 human...

As to cost, Illumina is advertising $1000 human genomes at 30X coverage. The first human genome sequenced by PacBio at 54X coverage costs around $60k-80k. The price difference is still considerable....
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