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Search: Posts Made By: Liy
Forum: General 06-20-2015, 01:29 PM
Replies: 1
Views: 1,061
Posted By Liy
solved awk 'FNR==NR{A[NR]=$0;next} ($0 in...

solved

awk 'FNR==NR{A[NR]=$0;next} ($0 in A){print A[$0]}' file2 file1
Forum: General 06-20-2015, 05:18 AM
Replies: 1
Views: 1,061
Posted By Liy
text file editing

Dear all,

I have a problem that i cannot solve and I hope someone here can help me.

I have two text files with one column of values.
Example:

File1:
67
94
Forum: Bioinformatics 02-24-2015, 06:38 AM
Replies: 1
Views: 1,126
Posted By Liy
Smile BWA MEM question

Dear all,

I just have a question about bwa mem alignment. I ran the following simple command:

bwa mem <fa> <fastq> -t 5

Before the alignment I checked the number of reads with fastqc and...
Forum: Bioinformatics 01-19-2015, 01:28 AM
Replies: 2
Views: 1,157
Posted By Liy
Thank you! Ill check this out!

Thank you! Ill check this out!
Forum: Bioinformatics 01-18-2015, 11:53 PM
Replies: 2
Views: 1,157
Posted By Liy
Viral sequences in hg19

Dear all,

I'm trying to obtain viral sequence loci in the human genome. Can anyone suggest an easy way to do this?

I found several endogenous retrovirus sites in papers, but i want to analyze...
Forum: Bioinformatics 04-30-2014, 01:52 AM
Replies: 7
Views: 7,401
Posted By Liy
Hi all, Can someone please tell me, how...

Hi all,

Can someone please tell me, how exactly handle bowtie2 the multiple aligned reads? I ran the following commad and the results showed that ~50% of my reads (10m) could align multiple times....
Forum: Bioinformatics 02-11-2014, 01:08 AM
Replies: 1
Views: 1,969
Posted By Liy
Same problem, could you figure it out? L

Same problem, could you figure it out?

L
Forum: Bioinformatics 02-10-2014, 12:21 PM
Replies: 3
Views: 1,587
Posted By Liy
motif genome wide

Hi all,

Can someone tell me how to get all the coordinate of a sequence motif coordinate genome wide? Prefered output is bed format.

Thanks!
L
Forum: Bioinformatics 01-30-2014, 04:57 AM
Replies: 2
Views: 1,118
Posted By Liy
Affy Tiling Array Analysis

Hi all,

Can someone help me suggest, an easy way to identify peaks from affymetrix ChIP-chip .CEL files?
I tried affy package (enviroment problem), and Starr. Is there any softwere, that can...
Forum: Bioinformatics 01-28-2014, 07:22 AM
Replies: 5
Views: 1,232
Posted By Liy
Thank you very much, all of you!

Thank you very much, all of you!
Forum: Bioinformatics 01-28-2014, 05:54 AM
Replies: 5
Views: 1,232
Posted By Liy
bash help

Hi there,

I cant figure it out how to solve a problem in unix, so a little help would be appritiated.

So, I want to delete a line (or swap the two column) only if the column3 is greater then...
Forum: Bioinformatics 12-27-2013, 02:37 AM
Replies: 2
Views: 4,965
Posted By Liy
Thank you!

Thank you!
Forum: Bioinformatics 12-27-2013, 02:08 AM
Replies: 2
Views: 4,965
Posted By Liy
Split Paired-End bam file

Hi all,

How can I split a paired-end bam file, to separate paired reads?

Paired.bam > Pair_1.bam Pair_2.bam

Thanks!
Forum: Bioinformatics 12-16-2013, 11:25 PM
Replies: 2
Views: 1,449
Posted By Liy
Hi, You can use bedtools random for example....

Hi,

You can use bedtools random for example. You can specify the length and the number of intervals you want.

http://bedtools.readthedocs.org/en/latest/content/tools/random.html

or
...
Forum: RNA Sequencing 12-06-2013, 01:05 AM
Replies: 15
Views: 7,729
Posted By Liy
Thanks Alex! Is these data normalized in...

Thanks Alex!

Is these data normalized in some way?

L
Forum: Bioinformatics 11-28-2013, 12:33 AM
Replies: 1
Views: 1,870
Posted By Liy
Create FixedStep Wig

Hi all,

I just want to know how to create a fixed step wig file from a bam file. I read a lot but couldnt find the answer.
I want to create several wigs with the same row and position with the...
Forum: Bioinformatics 10-31-2013, 07:55 AM
Replies: 2
Views: 2,159
Posted By Liy
Thank you!

Thank you!
Forum: Bioinformatics 10-30-2013, 02:28 AM
Replies: 2
Views: 2,159
Posted By Liy
Wig correlation

Hi all,

I've made several correlation with my ChIP-seq data (hg19) wig files (variable step) with ENCODE .bigWig files with wigCorrelate software. It makes the correlation, is this correalation...
Forum: Bioinformatics 07-15-2013, 01:53 AM
Replies: 0
Views: 1,581
Posted By Liy
Unhappy Agilent ChIP-chip data analysis

Dear all,

Recently, I've got several normalized Agilent (4x44k, Yeast) ChIP-chip data in .txt format. I would like to analyse it in R (peak calling, visualization, etc.), but i can't find a proper...
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