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Forum: Bioinformatics 01-01-2015, 09:43 AM
Replies: 0
Views: 802
Posted By modi2020
SVDetect Intrachromosomal Deletion

Hi Guys,

I ran SVDetect on Next generation paired end data and got the output but I am confused as to how to interpret the intrachromosomal deletions.
My understanding of the basic deletion...
Forum: Bioinformatics 04-14-2014, 04:02 PM
Replies: 17
Views: 6,227
Posted By modi2020
Dear Luc, Thank you for your advise. I have...

Dear Luc,

Thank you for your advise. I have actually trimmed up to 110 previously but the presence of kmers in the Fastqc report persisted. When I used the adapters set supplied by trimmomatic for...
Forum: Bioinformatics 04-14-2014, 03:54 PM
Replies: 17
Views: 6,227
Posted By modi2020
Dear Mastal, After following your advise I...

Dear Mastal,

After following your advise I am glad to say that it worked! I have attached the output of Fastqc herein.
I have basically used the file TruSeq3-PE-2.fa as adapters sequences and it...
Forum: Bioinformatics 04-13-2014, 02:43 PM
Replies: 17
Views: 6,227
Posted By modi2020
I have used the ILLUMINACLIP command to remove...

I have used the ILLUMINACLIP command to remove the kmers. My command was as follows:
java -Xmx15g -classpath trimmomatic-0.22.jar org.usadellab.trimmomatic.TrimmomaticPE -threads 4 -phred33 -trimlog...
Forum: RNA Sequencing 04-13-2014, 01:33 PM
Replies: 15
Views: 5,342
Posted By modi2020
Thank you for your quick reply mastal, I got...

Thank you for your quick reply mastal,

I got it now. I confused MINLEN and minAdapterLength.
So in the command "ILLUMINACLIP:adapters/TruSeq2-PE.fa:30:12:1:true"
there was no minAdapterLength...
Forum: RNA Sequencing 04-13-2014, 12:35 PM
Replies: 15
Views: 5,342
Posted By modi2020
Hi Toney, I noticed your ILLUMINACLIP...

Hi Toney,

I noticed your ILLUMINACLIP command and wanted to verify I got the manual correctly. So the manual say its:
ILLUMINACLIP:<fastaWithAdaptersEtc>:<seed mismatches>:<palindrome clip ...
Forum: Bioinformatics 04-11-2014, 01:37 PM
Replies: 17
Views: 6,227
Posted By modi2020
Dear Mastal, Thank you for your prompt...

Dear Mastal,

Thank you for your prompt reply.
I honestly thought that ILLUMINACLIP command was only for Overrepresented sequences e.g Illumina adapters. I will try using it and see what I get. ...
Forum: Bioinformatics 04-11-2014, 01:16 PM
Replies: 17
Views: 6,227
Posted By modi2020
Kmers remain even after trimmomatic trimming

Hi Guys,

I have Illumina NGS DNA 150 BP paired end reads.
My initial Fasqc report indicated the presence of Kmers towards the end of the reads at 145-147.
I used trimmomatic to trim them off....
Forum: Bioinformatics 04-01-2013, 03:15 PM
Replies: 31
Views: 12,661
Posted By modi2020
Thank you so much for your reply. I think I...

Thank you so much for your reply.
I think I finally figured it out.

best whishes
Forum: Bioinformatics 03-20-2013, 09:26 PM
Replies: 11
Views: 2,625
Posted By modi2020
Actually I think I got it. The way I did it is...

Actually I think I got it.
The way I did it is using a sliding window option. What I think I did is ask it to go through the sequence in a window of 4 bps, take the average score, if the average...
Forum: Bioinformatics 03-20-2013, 08:50 PM
Replies: 11
Views: 2,625
Posted By modi2020
Thank you for the explanation Jakie. I got the...

Thank you for the explanation Jakie. I got the idea now.
I tried to specify the quality after specifying the phred score and it didn't work though. To be specific I used -phred33 20
Is that what...
Forum: Bioinformatics 03-20-2013, 07:10 PM
Replies: 11
Views: 2,625
Posted By modi2020
Hi Jakie I have tried to run trimmomatic...

Hi Jakie

I have tried to run trimmomatic with the option -phred20 to get reads with quality scores of Q20 but it doesn't seem to like it. It runs with -phred33 though. In their website, they say...
Forum: Bioinformatics 03-20-2013, 04:11 PM
Replies: 31
Views: 12,661
Posted By modi2020
Hi Folks: I was wondering about the option...

Hi Folks:

I was wondering about the option -phred. I was told that a quality score above 20 should be ok for de novo assmbly reads but I could not force trimmomatic to accept the option -phred20....
Forum: Bioinformatics 03-20-2013, 09:48 AM
Replies: 11
Views: 2,625
Posted By modi2020
Thank you JackieBadger and mastal for your...

Thank you JackieBadger and mastal for your explaination.
I got the idea now.
Forum: Bioinformatics 03-20-2013, 08:43 AM
Replies: 11
Views: 2,625
Posted By modi2020
Hi, I was wondering for steps 2 and 3, how...

Hi,

I was wondering for steps 2 and 3, how many nucleotides would it trim from the start or end of the sequence. My intuition tells me its just one but I am not sure?
Forum: Bioinformatics 02-12-2013, 04:17 PM
Replies: 6
Views: 5,949
Posted By modi2020
Hi Krobison, I am having exactly the same...

Hi Krobison,

I am having exactly the same problem you were having.
Did you get to know how to solve it?

Thank you
Forum: Bioinformatics 01-30-2013, 09:16 PM
Replies: 0
Views: 1,552
Posted By modi2020
www.bribes.org seems to be offline (or gone)

Hi guys,

I am trying to add several packages in active state perl that depend on the bribes repository. For some reason the repository has been offline for at least 5 days now. Does anyone know...
Forum: Bioinformatics 12-03-2012, 08:45 PM
Replies: 0
Views: 1,212
Posted By modi2020
Obtaining UCSC Genomic sequence Given Genomic Coordinates

Hi Guys,

I want to import the ucsc Chr19 reference genome sequence for the horse genome on to R. I know I can do it using the BSgenome package. However,unfortunately they don't yet have the...
Forum: Introductions 05-27-2012, 08:29 AM
Replies: 22
Views: 25,118
Posted By modi2020
Hi Heisman, This clarifies the process a lot...

Hi Heisman,

This clarifies the process a lot to me. Thank you so much for your detailed answer and help with this.

Best
Forum: Introductions 05-25-2012, 11:15 PM
Replies: 22
Views: 25,118
Posted By modi2020
Hi Heisman, I Just need a simple...

Hi Heisman,

I Just need a simple clarification please.
Suppose you have a read like (AAACGGCGTTTCCC)
and you want to sequence it using Illumina paired end runs.
Does paired end mean you will...
Forum: Illumina/Solexa 05-25-2012, 10:42 PM
Replies: 11
Views: 6,606
Posted By modi2020
Thank you BAMseek for helping me with this. I...

Thank you BAMseek for helping me with this.
I have an inquiry though. Assuming the reads are 200 bp. suppose we read the ends only. How would we know the sequence in between?
Also, while sequencing...
Forum: Illumina/Solexa 05-25-2012, 03:21 PM
Replies: 11
Views: 6,606
Posted By modi2020
Hi guys... I am a bit confused about the way we...

Hi guys...
I am a bit confused about the way we deal with paired end reads...
Say we have a read that is AAACGCGCTTTCCC
does paired end mean we only sequence AAA and CCC?
how about the sequence...
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