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Search: Posts Made By: Hedi86
Forum: Bioinformatics 01-31-2020, 04:26 AM
Replies: 4
Views: 644
Posted By Hedi86
thank you we actually used two different...

thank you

we actually used two different kits for RRBS library preparation, I figured out that there is lots of short reads under 70 bp in the first method and using another method the peak of...
Forum: Bioinformatics 01-31-2020, 03:57 AM
Replies: 4
Views: 644
Posted By Hedi86
thank you Felix so i just imported the BAM...

thank you Felix

so i just imported the BAM files generated by Bismark into Seqmonk, without any quantification i can click on read length distribution histogram on data sets. but trimmed files...
Forum: Bioinformatics 01-30-2020, 05:47 AM
Replies: 4
Views: 644
Posted By Hedi86
length of uniquely mapped seq in Bismark

Dear all

Bismark reports the number of allignments with a unique best hit, is there a way to know what was the Length of those unique sequences ? for instance I have an RRBS library which after...
Forum: Bioinformatics 06-02-2019, 08:26 AM
Replies: 13
Views: 2,316
Posted By Hedi86
Dear Felix thank you for your time, we...

Dear Felix

thank you for your time, we really dont know why we have data alignment with Rat, we never had Rat samples in our lab. the platform used for DNA extraction never been exposed to rat...
Forum: Bioinformatics 06-02-2019, 04:23 AM
Replies: 13
Views: 2,316
Posted By Hedi86
thank you for your help yes and sorry i...

thank you for your help

yes and sorry i realized i have sent trimmed file. i have sent the raw file now again and if you have time i would appreciate your effort again.

i managed to get the...
Forum: Bioinformatics 05-28-2019, 03:34 AM
Replies: 13
Views: 2,316
Posted By Hedi86
thanks a lot, I just have sent you the files. ...

thanks a lot, I just have sent you the files.

Best
Forum: Bioinformatics 05-28-2019, 01:22 AM
Replies: 13
Views: 2,316
Posted By Hedi86
Hello again Felix after long time and...

Hello again Felix

after long time and sequencing twice, we never managed to identify the primers on Read 2 in our libraries. therefore we continued with another kit and this time we identified...
Forum: Bioinformatics 12-20-2018, 05:51 AM
Replies: 1
Views: 995
Posted By Hedi86
we contacted CLC and they confirmed that mapping...

we contacted CLC and they confirmed that mapping efficiency in CLC is unique and un unique mapping, thats why we ended up with 75%. they showed us how to extract only unique mapping and the results...
Forum: Bioinformatics 12-18-2018, 07:34 AM
Replies: 3
Views: 4,655
Posted By Hedi86
thank you for your replay for downstream...

thank you for your replay

for downstream analyses in Bismark i used both Val-trimmed-R1 and Val-trimmed-R2 files (because libraries prepared using NuGEN kit). however, bismark produced only one...
Forum: Bioinformatics 12-18-2018, 06:53 AM
Replies: 1
Views: 995
Posted By Hedi86
Cool RRBS mapping efficiency in CLC vs Bismark

Hi

we are working with RRBS data from bull sperm samples. previously we used Bismark mapper for pig data and the results were very good (around 60% mapping efficiency). however for bull data we...
Forum: Bioinformatics 08-19-2018, 11:27 PM
Replies: 13
Views: 2,316
Posted By Hedi86
Hello again Felix i just realized that...

Hello again Felix

i just realized that library been prepared using RRBS NuGEN Ovation kit which demands its own method of trimming. this time i got 29% mapping efficiency using default parameters....
Forum: Bioinformatics 08-15-2018, 02:27 AM
Replies: 2
Views: 1,324
Posted By Hedi86
thank you for your advice and help. in methylkit...

thank you for your advice and help. in methylkit using following command you can get coverage as well. but im wondering is it CpG coverage or read coverage? they used both definitions in their...
Forum: Bioinformatics 08-13-2018, 11:21 PM
Replies: 2
Views: 1,324
Posted By Hedi86
CpG sites in Bismark

Hello

im trying to calculate the percentage of covered CpG sites in my RRBS library and compare it with total CpG sites in reference genome. i got splitting report from Bismark (see bellow)
...
Forum: Bioinformatics 07-30-2018, 03:10 AM
Replies: 6
Views: 1,231
Posted By Hedi86
thanks alot for your explanation, now became more...

thanks alot for your explanation, now became more clear :)
Forum: Bioinformatics 07-30-2018, 02:58 AM
Replies: 6
Views: 1,231
Posted By Hedi86
really appreciate your comment so could we...

really appreciate your comment

so could we say that 0.04 as fold coverage is equal to 4X depth coverage, and could we say that read coverage is equal to mapping efficiency?

thanks again
Forum: Bioinformatics 07-30-2018, 01:58 AM
Replies: 6
Views: 1,231
Posted By Hedi86
thank you for your help. i tried to use...

thank you for your help.

i tried to use seqmonk, but i wasnt sure which file should i import (.fq file after trimming or COV file from bismark) ? in addition what is the correct pipeline in...
Forum: Bioinformatics 07-26-2018, 10:36 PM
Replies: 6
Views: 1,231
Posted By Hedi86
depth of coverage and read depth using Bismark

hello everyone

is it possible to calculate depth of coverage and read depth using Bismark ? if yes how and if No what is the best way to calculate depth of coverage and read of depth from RRBS...
Forum: Bioinformatics 07-26-2018, 03:24 AM
Replies: 13
Views: 2,316
Posted By Hedi86
Dear Felix thank you so much for your huge...

Dear Felix

thank you so much for your huge help, i really appreciate your time end effort.

i was suspected to contamination too as my very basic Blast experiment of trimmed reads (i removed...
Forum: Bioinformatics 07-24-2018, 05:36 AM
Replies: 13
Views: 2,316
Posted By Hedi86
strainge mapping efficency for paired end seq using Bismark

although similar issue been reported several times but i tried all the suggestions but problem still exist. Im working with RRBS data obtained from Cow sperm DNA. Standard illumine adapters and low...
Forum: Bioinformatics 06-26-2018, 08:38 AM
Replies: 3
Views: 4,655
Posted By Hedi86
trimming paired end reads using Trim galore

Dear all

im trying to trim paired-end RRBS illumina reads using Trim galore. as far as i understood, paired end reads must be trimmed using --paired option following by file names. i tried :...
Forum: Bioinformatics 10-26-2017, 05:45 AM
Replies: 0
Views: 655
Posted By Hedi86
Question Workflow and setting in Seqmonk

Dear all

im going to analyze bisulfite sequencing data and determine the DMR in my test and treatment groups. here is my workflow and setting for SeqMonk software but im not sure whether they are...
Forum: Bioinformatics 10-20-2017, 04:12 AM
Replies: 2
Views: 1,087
Posted By Hedi86
thank you so much for your help, the course is...

thank you so much for your help, the course is awesome :)

Thank you again
Forum: Bioinformatics 10-20-2017, 02:46 AM
Replies: 2
Views: 1,087
Posted By Hedi86
Cool best input file format for SeqMonk

hello

i am going to identify Differentially methylated regions (DMRs) using SeqMonk. as you know i can use different file format as my imported data. i used BAM, SAM, SAM sorted, COV files from...
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