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Search: Posts Made By: cliff
Forum: Bioinformatics 09-18-2011, 07:02 PM
Replies: 1
Views: 4,907
Posted By cliff
PCR duplicate removal for whole genome sequencing vs. whole exome sequencing

Hi

I did whole-genome sequencing and whole-exome sequencing on a whole-genome amplified (WGAd) sample and got 2% of reads removed as duplicates by whole-genome sequencing but 80% of reads removed...
Forum: Bioinformatics 07-07-2011, 01:20 PM
Replies: 0
Views: 1,177
Posted By cliff
how to find the genomic coordinate based on the amino acid change

Hi, I have lots of amino acid changes, for example, P94T on gene CDH1. Does anyone know an easy way to find its corresponding genomic coordinate in hg19?

Thanks

-C
Forum: Bioinformatics 02-18-2011, 04:44 PM
Replies: 4
Views: 5,471
Posted By cliff
Error "RG ID on SAMRecord not found in header" from Picard's MarkDuplicates.jar‏

I am trying the following command:

java -Xmx4g -jar /home/picard-tools-1.35/MarkDuplicates.jar INPUT=$dir/input.bam OUTPUT=$dir/output.bam TMP_DIR=/home/temp METRICS_FILE=PCR_duplicates...
Forum: Bioinformatics 12-15-2010, 12:37 PM
Replies: 15
Views: 6,629
Posted By cliff
Hi, Nirav99 Thanks! I tried your command and...

Hi, Nirav99

Thanks! I tried your command and still failed..
Forum: Bioinformatics 12-15-2010, 06:25 AM
Replies: 15
Views: 6,629
Posted By cliff
I specified a temporary directory which has...

I specified a temporary directory which has enough space by

java -Xmx4g -Djava.io.tmpdir=/home/temp -jar

it still failed...
Forum: Bioinformatics 12-13-2010, 07:31 AM
Replies: 15
Views: 6,629
Posted By cliff
thanks for getting back to me. I actually have...

thanks for getting back to me. I actually have 15TB left..
Forum: Bioinformatics 12-11-2010, 07:15 PM
Replies: 15
Views: 6,629
Posted By cliff
hi, nirav99 I got the same error "Mate...

hi, nirav99

I got the same error "Mate negative strand flag does not match read negative strand flag of mate" and I tried FixMateInformation as:

java -Xmx2g -jar FixMateInformation.jar...
Forum: Bioinformatics 10-23-2010, 07:16 PM
Replies: 5
Views: 1,897
Posted By cliff
Question about BED format - chromStart and End

I am a bit confused about the chromStart and chromEnd positions in the BED format.

According to UCSC:
chromStart - The starting position of the feature in the chromosome or scaffold. The...
Forum: Bioinformatics 10-07-2010, 03:25 PM
Replies: 13
Views: 9,925
Posted By cliff
wow...just noticed the latest responses.. Thanks...

wow...just noticed the latest responses.. Thanks very much for your suggestions and comments, especially to SVL, Johnathon , malachig, and steven!!!

You guys are awesome!
Forum: Bioinformatics 10-05-2010, 10:39 AM
Replies: 13
Views: 9,925
Posted By cliff
Hi, Johnathon Thanks for your response! I...

Hi, Johnathon

Thanks for your response! I know we can get exon coordinates from UCSC table browser. Do you know where we can get coordinates for promoter and splice sites?

-C
Forum: Bioinformatics 10-03-2010, 05:55 PM
Replies: 23
Views: 11,216
Posted By cliff
Hi, simonandrews I just noticed that the...

Hi, simonandrews

I just noticed that the SeqMonk Release Notes talks about SeqMonk v0.12.0 but it seems I can only find SeqMonk v0.11.0 online. Do you know where to find v0.12.0?

Thanks
Forum: Bioinformatics 10-03-2010, 09:49 AM
Replies: 13
Views: 9,925
Posted By cliff
Thanks! Do you know if there is any script or...

Thanks! Do you know if there is any script or online tool that can deal with data downloaded from UCSC? I am concerned with the possible conflict of the format or coordinate between ensembel and UCSC.
Forum: Bioinformatics 10-02-2010, 10:20 AM
Replies: 13
Views: 9,925
Posted By cliff
where to find coordinates for promter, splice site, splice regulatory site?

Hi, All

I am trying to look for coordinates of promoters, splice sites, and splice regulatory sites for a whole genome sequencing project. I want to know SNP distribution in those regions. Does...
Forum: Bioinformatics 10-01-2010, 07:55 AM
Replies: 23
Views: 11,216
Posted By cliff
Hi, golharam and simonandrews Thanks! I am...

Hi, golharam and simonandrews

Thanks! I am using WinXP. I will try to run SeqMonk on my desktop first to see if it works.

-c
Forum: Bioinformatics 09-29-2010, 06:40 PM
Replies: 23
Views: 11,216
Posted By cliff
hi, golharam How to use -X for X11 forwading...

hi, golharam

How to use -X for X11 forwading with SSH? I am not familiar with X11. I turned on "Tunnel X11 Connections" in ssh settings but it didn't work..
Forum: Bioinformatics 09-29-2010, 12:57 PM
Replies: 23
Views: 11,216
Posted By cliff
hi, simonandrews Do you have any experience...

hi, simonandrews

Do you have any experience in trying SeqMonk in linux? I use SSH to connect our linux server. I just downloaded SeqMonk to my directory and tried to launch it by using



but...
Forum: Bioinformatics 09-07-2010, 05:32 AM
Replies: 5
Views: 3,609
Posted By cliff
my error is the same. I added at the...

my error is the same. I added

at the beginning of bam2cfg.pl so my line 223 is your line 222.

Have you changed line 61 or 60 to




I installed three modules and changed line 61 but...
Forum: Bioinformatics 09-06-2010, 12:32 PM
Replies: 5
Views: 3,609
Posted By cliff
how to make BreakDancer's bam2cfg.pl work?

Dear All,

I hope someone here can help me figure out how to make BreakDancer's bam2cfg.pl work. I just downloaded the latest version of BreakDancer from...
Forum: Bioinformatics 07-19-2010, 07:52 AM
Replies: 9
Views: 36,983
Posted By cliff
mard: Thanks for your response! Is this 1000...

mard:

Thanks for your response! Is this 1000 genome hg19 reference sequence different from that one from UCSC? All the files I have been using were downloaded from UCSC and I hope there won't be...
Forum: Bioinformatics 07-16-2010, 12:00 PM
Replies: 9
Views: 36,983
Posted By cliff
Aleferna Thanks, I have that one too. I am...

Aleferna

Thanks, I have that one too. I am thinking of trying

cat chr*.fa > hg19.fa

But I am just not sure whether this concatenated hg19.fa is different from the one converted from...
Forum: Bioinformatics 07-16-2010, 11:17 AM
Replies: 9
Views: 36,983
Posted By cliff
Thanks, Thaley, I just found that page two. Here...

Thanks, Thaley, I just found that page two. Here is a question, how to use twoBitToFa to convert hg19.2bit to hg19.fa?

I just tried

./twoBitToFa hg19.2bit hg19.fa

but it said "Floating...
Forum: Bioinformatics 07-16-2010, 09:28 AM
Replies: 9
Views: 36,983
Posted By cliff
where to download hg19?

Dear All

I am wondering where to download hg19 reference files. I need to map my illumina reads to hg19 by using BWA.

All your help will be appreciated.

-C
Forum: Bioinformatics 06-12-2010, 06:30 PM
Replies: 1
Views: 3,731
Posted By cliff
SAMtools merge problem

I used "samtools sort" to sort three bam files and then used "samtools merge" to merge all of them. I am wondering whether I need sort the merged bam file again.

Thanks
Forum: Bioinformatics 06-12-2010, 06:15 PM
Replies: 12
Views: 14,125
Posted By cliff
I tried again java -Xmx2g -jar...

I tried again

java -Xmx2g -jar ~/picard-tools-1.21/MarkDuplicates.jar INPUT=test_sorted.bam OUTPUT=test_rmdup.bam METRICS_FILE=PCR_duplicates REMOVE_DUPLICATES=true

And I got this error:
...
Forum: Bioinformatics 06-12-2010, 10:12 AM
Replies: 12
Views: 14,125
Posted By cliff
How to use Picard's MarkDuplicates

I just tried Picard to remove PCR duplicates and used the test_sorted.bam (obtained by using samtools sort) as the input file. My following command

java -jar MarkDuplicates.jar test_sorted.bam...
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