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Search: Posts Made By: aslihan
Forum: Bioinformatics 07-20-2014, 09:18 PM
Replies: 4
Views: 2,808
Posted By aslihan
I think we need to trust the Tophat align_summary...

I think we need to trust the Tophat align_summary file to determine the number of reads since samtools flagstat reporting all multiple reads.
Forum: Bioinformatics 07-20-2014, 09:14 PM
Replies: 4
Views: 2,808
Posted By aslihan
same problem. Is there anyone to explain these...

same problem. Is there anyone to explain these differences??
Forum: Bioinformatics 10-06-2012, 10:01 PM
Replies: 16
Views: 12,217
Posted By aslihan
Hello, I created log2(FPKM tissueA/ FPKM tissueB)...

Hello, I created log2(FPKM tissueA/ FPKM tissueB) table for control 6sample and disease 7samples and would like to see significant differential genes.

log2(fpkmA/fpkmB) CTRL1.....6 ...
Forum: Bioinformatics 09-30-2012, 11:39 PM
Replies: 6
Views: 3,462
Posted By aslihan
perfect news :) Thank you.

perfect news :) Thank you.
Forum: RNA Sequencing 09-02-2012, 11:17 AM
Replies: 11
Views: 12,251
Posted By aslihan
Thank you for the explanation. I am wondering how...

Thank you for the explanation. I am wondering how can quantify antisense transcripts from non-strand Specific RNA seq ?

Thanks
Forum: Bioinformatics 09-02-2012, 11:06 AM
Replies: 1
Views: 1,305
Posted By aslihan
Quantifying antisense transcription from non-strand Specific RNA seq

Hello All,

I would like to learn more about how I can use non-strand specific RNA seq data to quantify antisense transcripts in mouse genome?

I really appreciate any guidance and help.

Thank...
Forum: RNA Sequencing 07-17-2012, 12:10 PM
Replies: 61
Views: 34,003
Posted By aslihan
I have same problem like starr and fed. ...

I have same problem like starr and fed.


myIDs<-read.table("gene_name.txt")

It works.There are 2 columns first: number 2nd column: gene_short_name

myGenes<-getGenes(cuff_data,myIDs)...
Forum: Bioinformatics 07-02-2012, 11:02 AM
Replies: 6
Views: 4,821
Posted By aslihan
I just opened the excel file and import...

I just opened the excel file and import counts_table.txt file and saved as csv file.


> countsTable <- read.table("/countstable/count_table_last.csv", sep=',', header=FALSE, row.names=1)
> head...
Forum: Bioinformatics 07-02-2012, 10:14 AM
Replies: 6
Views: 4,821
Posted By aslihan
HELP Count Table for DESeq

cat Join_counts_trimmed.txt | head

1/2-SBSRNA4 13 12 12 48
A1BG 12 2 7 12
A1BG-AS1 8 3 12 12
A1CF 2 3 0 1
A2LD1 29 33 47 47
A2M 21 36 19 6
A2ML1 8 11 6 16
A2MP1 0 0 1 0
Forum: Bioinformatics 06-29-2012, 11:12 AM
Replies: 13
Views: 6,098
Posted By aslihan
Hello, samtools sort -n accepted_hits.bam...

Hello,

samtools sort -n accepted_hits.bam accepted_hits_sorted

samtools view -h accepted_hits_sorted.bam > accepted_hits_sorted.sam

htseq-count -m intersection-strict --stranded=no -t exon...
Forum: Bioinformatics 01-27-2012, 11:58 AM
Replies: 6
Views: 11,593
Posted By aslihan
Thank you. Sorry for my late. I will try them.

Thank you. Sorry for my late. I will try them.
Forum: Bioinformatics 12-02-2011, 09:40 AM
Replies: 10
Views: 4,261
Posted By aslihan
Hi Ih3 Could you write the command for it?...

Hi Ih3

Could you write the command for it? Where I put -D and -S?

samtools mpileup -EuDSf *.fa s1.sorted.bam s2.sorted.bam
bcftools view -bvcg
bcftools/vcfutils.pl varFilter -D100

Thanks
Forum: Bioinformatics 12-01-2011, 10:41 AM
Replies: 3
Views: 3,401
Posted By aslihan
Did you find a solution to your problem? I have...

Did you find a solution to your problem? I have also similar questions.

Thanks
Forum: Bioinformatics 11-29-2011, 01:39 PM
Replies: 3
Views: 2,513
Posted By aslihan
you can use samtools mpileup to compare 2 vcf...

you can use samtools mpileup to compare 2 vcf files at the same time.
Forum: Bioinformatics 11-28-2011, 01:10 PM
Replies: 4
Views: 1,977
Posted By aslihan
Could you answer this question? I have also...

Could you answer this question? I have also similar question?
Forum: Bioinformatics 11-21-2011, 12:24 PM
Replies: 6
Views: 11,593
Posted By aslihan
how to annotate VCF files created by bcftools view?

I have 1 big vcf files which compares 12 samples by using samtools mpileup. And I would like annotate them? my reference genome is Hg19. How can annotate VCf files ?

Could you write commands and...
Forum: Bioinformatics 11-03-2011, 10:18 PM
Replies: 28
Views: 7,839
Posted By aslihan
Hi Chris, Thanks so much for your comments....

Hi Chris,

Thanks so much for your comments. I will read them. I hope I will fıgure out soon.

For example, I would like to see whether individual and different tissue differences or not between...
Forum: Bioinformatics 11-02-2011, 10:31 AM
Replies: 28
Views: 7,839
Posted By aslihan
Hi I am also working for SNP differences between...

Hi I am also working for SNP differences between 2 different cell lines which is got from 3 disease and 3 normal individual. First I did bowtie for alignment. Then I used samtools mpileup for...
Forum: Bioinformatics 11-01-2011, 08:13 AM
Replies: 1
Views: 3,153
Posted By aslihan
samtools mpileup and bcftools command lines to compare individual differences?

Which parameters are you using for samtools mpileup and bcftools to compare individual SNP differences?

Could you write your commands?

I am using:

samtools mpileup -ugf *.fa *.bam *.bam...
Forum: Bioinformatics 10-24-2011, 12:50 PM
Replies: 7
Views: 2,594
Posted By aslihan
How to use dp4 values ??

How to use dp4 values ??
Forum: Bioinformatics 10-24-2011, 08:11 AM
Replies: 14
Views: 5,616
Posted By aslihan
mpileup multiple samples - individual DP4/AF1 values

Hi,

I am calling SNP from multiple individuals using mpileup. I was wondering whether it is possible to get DP4 and AF1 values for each individual? I currently have DP4 and AF1 values for the...
Forum: Bioinformatics 10-04-2011, 08:19 AM
Replies: 3
Views: 2,295
Posted By aslihan
mpileup multiple samples - individual DP4/AF1 values

I have the same question. How can we get dp4 values for each individual. I wrote a command for it but it still keeps the main dp4 an dp values inside.

I am waiting for your reply!
Forum: Bioinformatics 07-22-2011, 10:33 AM
Replies: 3
Views: 3,792
Posted By aslihan
Samtools-mpileup

Dear all,

I used samtools mpileup in order to call the variants to compare my 12 samples. However it is hard to pick real and more confident heterozygous SNPs. I dont know how to eliminate...
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