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Search: Posts Made By: Mali Salmon
Forum: Bioinformatics 01-26-2014, 10:23 PM
Replies: 1
Views: 2,584
Posted By Mali Salmon
Hello Laura I see there were no replies to your...

Hello Laura
I see there were no replies to your post.
Have you managed to calculate dn/ds genome-wide?
I have bam as well as vcf files and I am interested with the average dN/dS value. Any tips?...
Forum: Genomic Resequencing 07-17-2013, 01:10 AM
Replies: 1
Views: 1,729
Posted By Mali Salmon
large indels in targeted sequencing

Hello List
We would like to find large deletions and insertions (>30bp) in targeted sequencing data. We are wondering which technology to use for that purpose. Ion torrent? illumina? single or...
Forum: RNA Sequencing 07-09-2013, 08:29 AM
Replies: 2
Views: 6,034
Posted By Mali Salmon
Thanks dpryan for your reply. The reason I am...

Thanks dpryan for your reply.
The reason I am interested with normalizing for that bias is because I have two different patterns of this bias in my samples.
I looked at the cqn package and as you...
Forum: RNA Sequencing 07-09-2013, 04:46 AM
Replies: 2
Views: 6,034
Posted By Mali Salmon
random hexamer bias

Hello list
Do you know if HTSeq/DESeq or edgeR account for the random hexamer bias?
If not, what would be an easy way to normalize for that bias prior of running DESeq?
Thanks
Mali
Forum: Literature Watch 10-25-2012, 12:08 PM
Replies: 4
Views: 11,060
Posted By Mali Salmon
Hi Eagle_Eye I just came across your post, and...

Hi Eagle_Eye
I just came across your post, and I am wondering if you managed to use PeakAnalyzer. If not I would love to help you out. Just send me the two files (links above don't work) to my...
Forum: Metagenomics 09-11-2012, 12:02 PM
Replies: 1
Views: 1,492
Posted By Mali Salmon
How deep to sequence?

Hi All
A friend of mine would like to find a specific virus from sludge samples, but she has no idea how deep she should sequence in order to actually see viral reads. The proportion between the...
Forum: Bioinformatics 05-23-2012, 01:28 AM
Replies: 24
Views: 5,900
Posted By Mali Salmon
Hello sasignor I am wondering if you diagnosed...

Hello sasignor
I am wondering if you diagnosed the problem
I am facing a similar issue, and would love to hear about your progress
Thanks
Forum: Bioinformatics 02-12-2012, 03:38 AM
Replies: 5
Views: 4,811
Posted By Mali Salmon
Thanks ETHANol for your reply. Can you explain...

Thanks ETHANol for your reply. Can you explain more why ChIP-seq pipeline is not suitable for RNA-based data, what is the reason for the high false-positive rate?
I have RNA-IP sample and RNA-Input...
Forum: Bioinformatics 02-12-2012, 03:32 AM
Replies: 5
Views: 5,480
Posted By Mali Salmon
Hi I would like to try your software for mouse...

Hi
I would like to try your software for mouse RIP-seq data. I am interested with finding peaks enriched in IP compared with Input. Is it possible with PyCRAC?
My mail shalmom1@gmail.com
Thanks...
Forum: Bioinformatics 02-12-2012, 03:12 AM
Replies: 5
Views: 4,811
Posted By Mali Salmon
CLIP/RIP-seq peak finding

A question to all users that run CLIP/RIP-seq and then try to find peaks in their data.
Since I couldn't find any specific tool for finding peaks in RNA-based data, I have decided to use the...
Forum: Bioinformatics 01-18-2012, 05:39 AM
Replies: 138
Views: 75,693
Posted By Mali Salmon
Wow, thanks a lot Peter for the helpful...

Wow, thanks a lot Peter for the helpful information
Mali
Forum: Bioinformatics 01-18-2012, 05:00 AM
Replies: 138
Views: 75,693
Posted By Mali Salmon
Thanks a lot Peter for quick reply. What do you...

Thanks a lot Peter for quick reply.
What do you mean by "single-exome" analysis? Do you mean single-end reads (as in my case) or single sample?
I actually have data from 4 patients, and I thought...
Forum: Bioinformatics 01-18-2012, 03:15 AM
Replies: 138
Views: 75,693
Posted By Mali Salmon
Hi All I have been trying to follow the...

Hi All
I have been trying to follow the exome-analysis pipeline written by ulz_peter (thanks petter for this clear and nice document). I have encountered the same problem as pc2009open when trying...
Forum: RNA Sequencing 06-27-2011, 09:57 AM
Replies: 0
Views: 1,852
Posted By Mali Salmon
ambiguous RNA-IP-seq reads in yeast

Hi All
I got some yeast RNA-IP-seq data from two conditions to analyze. I would like to do differential expression analysis by comparing the counts of the IP samples directly (without the using of...
Forum: Bioinformatics 06-14-2011, 04:17 AM
Replies: 16
Views: 6,257
Posted By Mali Salmon
I would like to try your scripts for CLIP-seq ...

I would like to try your scripts for CLIP-seq
Thanks
Mali
Forum: 454 Pyrosequencing 05-08-2011, 10:22 PM
Replies: 0
Views: 2,179
Posted By Mali Salmon
MIDs trimming

Hi All
I am trying to split multiplexed 454 data using sfffile, and trim the MIDs. The core facility used the same MID sequence in the 5' and 3', but when I run sfffile, it removes only the MID in...
Forum: Genomic Resequencing 05-05-2011, 01:14 AM
Replies: 14
Views: 5,480
Posted By Mali Salmon
I suppose they used both forward and reverse...

I suppose they used both forward and reverse adapters as primers for PCR, so you get fragments from both strands
Mali
Forum: Genomic Resequencing 05-04-2011, 03:51 AM
Replies: 14
Views: 5,480
Posted By Mali Salmon
As I understood it (from the experimentalist who...

As I understood it (from the experimentalist who did the capturing), the baits probe one strand but next there was a PCR amplification step (using the adapter indexes), so the sequenced fragments are...
Forum: Bioinformatics 04-13-2011, 12:46 AM
Replies: 0
Views: 2,275
Posted By Mali Salmon
5' bias in Illumina captured sequecning

Hi All
We performed captured DNA sequencing of all exons belonging to 10 genes using MYselect kit (from MYcroarray company).
The sequencing was done using both Illumina and 454 platforms. When we...
Forum: Genomic Resequencing 03-23-2011, 02:19 AM
Replies: 14
Views: 5,480
Posted By Mali Salmon
Thank you guys for your reply. The data I have...

Thank you guys for your reply.
The data I have are from people the carry a known heterozygous mutation, and we want to check if we can find this mutation using capture+sequencing. We also expect to...
Forum: Genomic Resequencing 03-23-2011, 12:56 AM
Replies: 14
Views: 5,480
Posted By Mali Salmon
SNP calling for captured sequence data

Hi All
I am currently analysing captured sequence data (DNA sequencing using illumina platform), with the aim of finding somatic mutations.
Can you please advice on the following issues:
1. Shall...
Forum: Bioinformatics 02-17-2011, 12:51 AM
Replies: 14
Views: 9,081
Posted By Mali Salmon
Thanks nil for your reply, but I haven't used the...

Thanks nil for your reply, but I haven't used the -b option, my input read files are fastq
Any other idea?
Mali
Forum: Bioinformatics 02-16-2011, 02:28 AM
Replies: 14
Views: 9,081
Posted By Mali Salmon
bwa sampe error

Hi
I'm trying to generate SAM alignment file using BWA version 0.5.9-r16.
I first aligned successfully paired-end reads to the reference using aln:
bwa aln ref.fasta s_1.fq > s1.aln
bwa aln...
Forum: Bioinformatics 02-07-2011, 04:42 AM
Replies: 3
Views: 2,976
Posted By Mali Salmon
Got the same error (using the same version), even...

Got the same error (using the same version), even without using -r
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