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Search: Posts Made By: Layla
Forum: 454 Pyrosequencing 12-20-2009, 04:30 AM
Replies: 13
Views: 7,092
Posted By Layla
Nope, Sorry! I am no longer working on this...

Nope, Sorry! I am no longer working on this project
Forum: Bioinformatics 11-27-2009, 02:09 AM
Replies: 5
Views: 4,608
Posted By Layla
Thank you for your reply kmcarr. According...

Thank you for your reply kmcarr.

According to my calculations from medip-seq on the human genome, theoretically I should not have any duplicates :D

The mates of these reads have a different...
Forum: Bioinformatics 11-23-2009, 06:24 AM
Replies: 5
Views: 4,608
Posted By Layla
Thank you for your quick response dawe :) L

Thank you for your quick response dawe :)
L
Forum: Bioinformatics 11-23-2009, 05:44 AM
Replies: 5
Views: 4,608
Posted By Layla
Solexa - same sequence but unique identifier

Hi all,

I am seeing this data from a paired end solexa run (pipeline 1.4). The sequence is identical, yet the identifiers (tile# on the flowcell, x and y coordinates) are different. In Bowtie...
Forum: Bioinformatics 11-20-2009, 08:20 AM
Replies: 3
Views: 3,361
Posted By Layla
Quick question, How does Bowtie deal with...

Quick question,

How does Bowtie deal with paired end reads where both ends align to different chromosomes? I believe maq gives various flags to identify such reads.

Thanks,
L
Forum: Bioinformatics 11-20-2009, 07:37 AM
Replies: 3
Views: 3,361
Posted By Layla
Hi Ben, Thanks for your reply. I've got...

Hi Ben,

Thanks for your reply. I've got myself a little muddled with the output. I used the -m1 -k1 option but I was worried I might be missing reads that had 1MM or 2MM as these would go...
Forum: Bioinformatics 11-20-2009, 06:01 AM
Replies: 3
Views: 3,361
Posted By Layla
Reliability

I am comparing the output from Bowtie and maq and using the command below I get a total of 147-e6 alignments for 34-e6 reads. After rigorous filtering, I have half the numbers of reads mapped to...
Forum: Bioinformatics 11-12-2009, 08:45 AM
Replies: 8
Views: 2,541
Posted By Layla
Hi all, I have downloaded build hg18 from...

Hi all,

I have downloaded build hg18 from ucsc.

command to build the index:
./bowtie-build -f chr1.fa chr2.fa chr3.fa chr4.fa chr5.fa chr6.fa chr7.fa chr8.fa chr9.fa chr10.fa chr11.fa...
Forum: Bioinformatics 11-12-2009, 04:17 AM
Replies: 8
Views: 2,541
Posted By Layla
Hi Ben, I receive the same errors wether I...

Hi Ben,

I receive the same errors wether I use curl/wget or click on the h_sapiens_asm.ebwt.1.zip file from
a)ftp://ftp.cbcb.umd.edu/pub/data/bowtie_indexes/h_sapiens_asm.ebwt.1.zip...
Forum: Bioinformatics 11-11-2009, 02:28 AM
Replies: 13
Views: 4,385
Posted By Layla
Cool From looking into Bowtie's defaults --phred33...

From looking into Bowtie's defaults --phred33 -quals is "on" and hence assumes you are providing reads in the standard sanger format (phred33). If you are providing data with quality scores in...
Forum: Bioinformatics 11-10-2009, 05:24 AM
Replies: 8
Views: 2,541
Posted By Layla
unzipping human bowtie indexes

Does anyone have a solution to unzipping the human index files needed for bowtie taken from http://bowtie-bio.sourceforge.net/md5s.shtml.

unzip h_sapiens_asm.ebwt.1.zip
Error:...
Forum: Bioinformatics 11-09-2009, 08:39 AM
Replies: 1
Views: 4,184
Posted By Layla
hg18 or hg19

Does anybody know the difference between the following files for Bowtie?
File: h_sapiens_37_asm.ebwt.zip (27-08-09) and
File: h_sapiens_asm.ebwt.zip (18-02-09)
Files found from:...
Forum: Bioinformatics 11-09-2009, 07:43 AM
Replies: 13
Views: 4,385
Posted By Layla
Just seen it! Thanks L

Just seen it!

Thanks

L
Forum: Bioinformatics 11-09-2009, 07:28 AM
Replies: 13
Views: 4,385
Posted By Layla
BOWTIE input

Does bowtie need to have reads in the standard sanger format or can it accept the default file created from the 1.4 illumina pipeline in which the quals are not standard sanger?

Cheers

L
Forum: Bioinformatics 11-02-2009, 08:16 AM
Replies: 514
Views: 211,053
Posted By Layla
comparable parameters with maq

Hi Ben,

Excellent work with Bowtie - looking forward to cutting down data processing time. Working on a project in which I have used maq, but for subsequent paired end medip-seq of 45 bases I...
Forum: Bioinformatics 09-09-2009, 07:44 AM
Replies: 514
Views: 211,053
Posted By Layla
Im a newbie to Bowtie....tired of the counting...

Im a newbie to Bowtie....tired of the counting down the hours using MAQ.

Currently building an index using Bowtie. What is the difference between
h_sapiens_asm.ebwt.zip and
h_sapiens.ebwt.zip
...
Forum: Bioinformatics 09-04-2009, 08:51 AM
Replies: 7
Views: 1,873
Posted By Layla
Great, but would you know of any way to speed maq...

Great, but would you know of any way to speed maq up? Even chunks of 2 million take a few days as I am running the .map command simultaneously. If not, not a problem.

Cheers
L
Forum: Bioinformatics 09-04-2009, 08:31 AM
Replies: 7
Views: 1,873
Posted By Layla
Thank you for your reply I have 10 patients...

Thank you for your reply
I have 10 patients each generate 15 .map files

I split them into pairs of 1 million (total 2 million reads) to speed up maq alignment.

L
Forum: Bioinformatics 09-04-2009, 07:27 AM
Replies: 7
Views: 1,873
Posted By Layla
maq merge limit

Hi,

Is there a limit to the number of map files that can be merged using
./maq mapmerge? If so, is there a way to overcome this for short paired end reads?

Cheers

L
Forum: Bioinformatics 06-26-2009, 01:17 AM
Replies: 57
Views: 39,972
Posted By Layla
maq to GFF2 format

Hi,

I know this is quite an old thread but useful for me at this moment.
Searching for a method to convert a maq alignment (to human ref genome) output from me-dip seq to GFF2 format for batman...
Forum: Bioinformatics 06-23-2009, 01:22 AM
Replies: 3
Views: 2,047
Posted By Layla
Thanx for your reply. I used the inbuilt...

Thanx for your reply.
I used the inbuilt command in maq:
./maq mapview out.map > out.txt ---> QC and filter
The pileup cannot accept the out.txt file I have cleaned up. It requires a binary.map...
Forum: Bioinformatics 06-19-2009, 08:01 AM
Replies: 3
Views: 2,047
Posted By Layla
back to binary

I converted a binary out.map file after a maq alignment to .txt and filtered for unreliable data. Attempting to do a maq pileup on the cleaned data, but pileup requires a .map file.

How do you...
Forum: 454 Pyrosequencing 06-16-2009, 04:50 AM
Replies: 5
Views: 3,821
Posted By Layla
50% lower case bases

Thank you for the information kmcarr.

I carried out a simple sffinfo -s file1.sff > file1.fna command without the -n option to get to this file. The fact that 454 has marked for these bases to be...
Forum: 454 Pyrosequencing 06-16-2009, 02:14 AM
Replies: 5
Views: 3,821
Posted By Layla
Titanium upper and lower case bases

Seeing a read like this from 454 Titanium shotgun experiment using DNA from a capture array.
...
Forum: Bioinformatics 06-12-2009, 07:01 AM
Replies: 14
Views: 14,427
Posted By Layla
Thankyou Jonathon and Zee, I guess this...

Thankyou Jonathon and Zee,

I guess this should be good enough. Split both files into 2 million chunks and then run the following command 5 times..
./maq match out.map all_chrom.bfa...
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