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Search: Posts Made By: dejavu2010
Forum: Bioinformatics 08-25-2014, 01:08 PM
Replies: 5
Views: 3,985
Posted By dejavu2010
where can i find the old python script?

where can i find the old python script?
Forum: Bioinformatics 03-18-2014, 07:46 AM
Replies: 6
Views: 3,285
Posted By dejavu2010
where can i get genome gc content

I am trying to use RNA-SeQC for a mouse rnaseq dataset. the program requires mouse gc content file. Where can i download it or how can i generate it by myself? Thanks a lot.
Forum: Bioinformatics 07-15-2013, 12:05 AM
Replies: 1
Views: 772
Posted By dejavu2010
general but important concepts

I have questions about some concepts:
1. In the reference human genome, i assume the position is relevant to the end of chromosome, which some times refers to pter, qter. I guess all position in the...
Forum: RNA Sequencing 04-18-2013, 12:07 AM
Replies: 7
Views: 3,556
Posted By dejavu2010
more questions

what is hap region? thx
Forum: Bioinformatics 06-20-2012, 03:26 PM
Replies: 1
Views: 1,489
Posted By dejavu2010
how to calculate gc content for every single genes in a genome-wide scale

how to calculate gc content for every single genes in a genome-wide scale? for example, RNA-seq needs adjust GC content for individual genes. How can I quickly calculate gc contents for human...
Forum: Bioinformatics 05-22-2012, 08:49 AM
Replies: 15
Views: 24,419
Posted By dejavu2010
I had the same question. First time, I treated 3...

I had the same question. First time, I treated 3 biological replicates as a group with "," to separate, with -L KO, WT. Second time, I treated every single sample with a condition, but labeled -L KO,...
Forum: Bioinformatics 04-24-2012, 07:41 PM
Replies: 6
Views: 8,440
Posted By dejavu2010
i mean how to create that file for other species,...

i mean how to create that file for other species, for example, mouse
Forum: Bioinformatics 04-24-2012, 05:59 PM
Replies: 6
Views: 8,440
Posted By dejavu2010
jon, thx. I checked your website, really helpful....

jon, thx. I checked your website, really helpful. the question i have now is how to create ribosome_locations.txt? thx
Forum: Bioinformatics 04-23-2012, 12:05 PM
Replies: 6
Views: 8,440
Posted By dejavu2010
co-ask

co-ask the same question
Forum: Bioinformatics 03-21-2012, 01:22 PM
Replies: 29
Views: 11,389
Posted By dejavu2010
i feel that Trimmomatic index your reads based on...

i feel that Trimmomatic index your reads based on input order, not lane_position_... combination, i tested one un matched dataset, they can not handle it.
Forum: Bioinformatics 02-28-2012, 03:08 PM
Replies: 12
Views: 5,718
Posted By dejavu2010
thx

it works, but with a little bit pain that it only works for a <4gb.
Forum: Bioinformatics 02-28-2012, 02:51 PM
Replies: 29
Views: 11,389
Posted By dejavu2010
thx. everybody, i got it resolved

thx. everybody, i got it resolved
Forum: Bioinformatics 02-28-2012, 09:56 AM
Replies: 29
Views: 11,389
Posted By dejavu2010
Hi my process got killed perl...

Hi

my process got killed

perl mergeShuffledFastqSeqs.pl -f1 2044-BH-1_1_sequence.txt -f2 2044-BH-1_2_sequence.txt -r '^@(\S+)\s[1|2]\S+$' -o 2044-BH-1 -t

Loading the first file...Killed
...
Forum: Bioinformatics 02-27-2012, 02:47 PM
Replies: 29
Views: 11,389
Posted By dejavu2010
hi azneto, how to setup regular expression like...

hi azneto, how to setup regular expression like the following
@HWI-ST829:138:D071VACXX:1:1101:1131:2048 1:N:0:ATCACG.

Thanks.
Forum: Bioinformatics 02-27-2012, 09:27 AM
Replies: 4
Views: 2,819
Posted By dejavu2010
1145LJZ0007_read1.txt is not original. The...

1145LJZ0007_read1.txt is not original. The original is .txt.gz. sorry for confusion.
Forum: Bioinformatics 02-27-2012, 09:25 AM
Replies: 4
Views: 2,819
Posted By dejavu2010
I found the actual cause for that problem. Since...

I found the actual cause for that problem. Since when we demultiplex sample, we limit reads number 16000000, and gunzip. Later on we concatenate them. Since Trimmomatic is a JAVA program which, I...
Forum: Bioinformatics 02-24-2012, 06:43 PM
Replies: 29
Views: 11,389
Posted By dejavu2010
program which can make a pair end to have equal number of sequence

i have a PE100, the problem is some tiles of read 2 are corrupted and it caused un even number of reads in read 1 and read 2. Are there any programs which can match up sequences from both reads and...
Forum: Bioinformatics 02-24-2012, 06:33 PM
Replies: 5
Views: 2,757
Posted By dejavu2010
Actually I have concatenate those 12 files into a...

Actually I have concatenate those 12 files into a big file and then upload it to FastQC, but it still only showed 16m reads.
michael
Forum: Bioinformatics 02-24-2012, 02:26 PM
Replies: 5
Views: 2,757
Posted By dejavu2010
fastqc read limit?

I have a question about Trimmomatic.

I have a PE 100 reads from hiseq 2000, 100PE reads =166,867,542 PE reads. when i opened it by fastqc, it only shows total sequence:16000000.
which CASAVA...
Forum: Bioinformatics 02-24-2012, 02:24 PM
Replies: 4
Views: 2,819
Posted By dejavu2010
question about Trimmomatic

I have a PE 100 reads from hiseq 2000, 100PE reads =166,867,542 PE reads. when i opened it by fastqc, it only shows total sequence:16000000. Anyway, I just wanted to eliminate adapter sequences by...
Forum: Illumina/Solexa 01-12-2012, 02:21 PM
Replies: 6
Views: 3,315
Posted By dejavu2010
Anyone has update about this post? I have the...

Anyone has update about this post? I have the same problem
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