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Search: Posts Made By: husamia
Forum: Bioinformatics 11-15-2016, 12:50 PM
Replies: 34
Views: 131,078
Posted By husamia
"it depends on the data in question". I suggest...

"it depends on the data in question". I suggest remove duplicates and see how it affects the overall quality. Then, decide weather removing duplicates is useful.
Forum: Illumina/Solexa 10-20-2016, 10:53 AM
Replies: 2
Views: 2,708
Posted By husamia
it depends what the rest of 75-85% is. Try to...

it depends what the rest of 75-85% is. Try to size select before sequencing, this gets ride of small fragments <150 that may be lost due to adapter contamination
Forum: Bioinformatics 10-20-2016, 10:19 AM
Replies: 9
Views: 1,817
Posted By husamia
if R1 and R2 are the paired sequences, then...

if R1 and R2 are the paired sequences, then should be count R1 = count R2 = number of clusters
Forum: General 10-20-2016, 10:14 AM
Replies: 1
Views: 2,852
Posted By husamia
You might try free VariantInterpreter from...

You might try free VariantInterpreter from Illumina
https://variantinterpreter.informatics.illumina.com
Forum: Bioinformatics 10-20-2016, 10:07 AM
Replies: 9
Views: 1,817
Posted By husamia
for pre-alignment counts you could count the...

for pre-alignment counts you could count the number of lines in the FASTQ files and divide by 4. I use wc -l
Forum: Bioinformatics 03-22-2013, 07:39 PM
Replies: 10
Views: 5,964
Posted By husamia
I also use the average depth of X and Y

I also use the average depth of X and Y
Forum: Bioinformatics 09-13-2012, 06:26 PM
Replies: 6
Views: 4,181
Posted By husamia
I use Mutalyzer which provides webservice...

I use Mutalyzer which provides webservice https://mutalyzer.nl/positionConverter
Forum: General 08-08-2012, 04:22 PM
Replies: 11
Views: 12,454
Posted By husamia
Try optimus primer http://op.pgx.ca/

Try optimus primer http://op.pgx.ca/
Forum: General 08-08-2012, 03:36 PM
Replies: 2
Views: 2,061
Posted By husamia
There are many public database that will allow...

There are many public database that will allow you to do this. Here is a small list

http://www.ncbi.nlm.nih.gov/SNP/
http://www.ensembl.org/biomart/
http://hapmap.ncbi.nlm.nih.gov/biomart/

...
Forum: Bioinformatics 07-09-2012, 10:32 AM
Replies: 5
Views: 3,083
Posted By husamia
I suggest using native linux tools such as grep,...

I suggest using native linux tools such as grep, sed, awk in multithreaded environment also 64 bit may be useful in some applications where it is supported. There is option of using CUDA with GPU to...
Forum: Bioinformatics 03-16-2012, 07:21 PM
Replies: 5
Views: 2,767
Posted By husamia
I agree. there is no way to know which reads at...

I agree. there is no way to know which reads at mt so you have to align first.
Forum: 454 Pyrosequencing 03-16-2012, 07:16 PM
Replies: 11
Views: 8,708
Posted By husamia
the coverage is never consistent it ranges from 0...

the coverage is never consistent it ranges from 0 to few hundred so when you say 30x coverage its meaningless, don't you agree?
Forum: Bioinformatics 02-05-2012, 02:34 PM
Replies: 4
Views: 1,868
Posted By husamia
I think this is great project. Its going to take...

I think this is great project. Its going to take sometime to think about it.

The big question is phasing. Do you or not know the phase?
I seems from your post that you don't know the phase then...
Forum: Bioinformatics 01-23-2012, 06:39 AM
Replies: 2
Views: 2,038
Posted By husamia
have you tried to look at the sequence to see if...

have you tried to look at the sequence to see if its the same?
Forum: Bioinformatics 01-23-2012, 06:03 AM
Replies: 11
Views: 11,349
Posted By husamia
I mentioned the wrong function, I modified my...

I mentioned the wrong function, I modified my response above to reflect the correct reference function. Sorry for confusion
Forum: Bioinformatics 01-20-2012, 01:32 PM
Replies: 11
Views: 11,349
Posted By husamia
I mentioned the wrong function I meant to mention...

I mentioned the wrong function I meant to mention Galaxy with the Intersect function in the operate on genomic intervals functions
here is example...
Forum: Bioinformatics 01-04-2012, 11:55 AM
Replies: 36
Views: 19,212
Posted By husamia
FASTQ is the raw reads with qualities. SAM is...

FASTQ is the raw reads with qualities. SAM is format to describe reads and their alignment. This was hinted in the previous respond above. It seems you've got to align the reads first if you just...
Forum: Bioinformatics 01-04-2012, 11:48 AM
Replies: 0
Views: 1,861
Posted By husamia
NCBI RefSeq "unclassified transcription discrepancy"

I wasn't sure if this forum would have discussed this before or would be a good place to discuss but I am sure some may be able to help and others may benifit. I searched and couldn't find anything. ...
Forum: Illumina/Solexa 11-10-2011, 08:52 AM
Replies: 1
Views: 1,099
Posted By husamia
adding date stamp to standard

I did a search and I didn't find anybody discussing this so I am posting it here for first time.

Why datestamp has not been added to the FASTQ standard format? its causing me alot of headache...
Forum: Bioinformatics 10-11-2011, 01:08 PM
Replies: 14
Views: 8,458
Posted By husamia
when you said you have pooled samples, I was...

when you said you have pooled samples, I was suprised. I thought you were supposed to demultiplex your pooled samples before aligning to any reference. Otherwise you don't know which sample is which....
Forum: Illumina/Solexa 09-21-2011, 10:27 AM
Replies: 6
Views: 7,754
Posted By husamia
Let me just make sure I am on the right page...

Let me just make sure I am on the right page before giving my opinion. your referring to Nextera vs. TruSeq prep kit, correct?
if so, I think there is difference since it involves the adding of...
Forum: RNA Sequencing 07-21-2011, 06:07 AM
Replies: 6
Views: 3,257
Posted By husamia
Thanks for explaining I like to clarify to...

Thanks for explaining I like to clarify to myself. Is the reason for the replicates to account for the bias created by the enrichment and other experiment bias? or they are different replicates? I...
Forum: RNA Sequencing 07-19-2011, 08:12 AM
Replies: 6
Views: 3,257
Posted By husamia
I may have some advice. Can you clarify what you...

I may have some advice. Can you clarify what you want to compare as "differential expression"?
If you measure expression as read count per mir as I understand to be the case but correct me if I am...
Forum: Bioinformatics 07-15-2011, 08:48 AM
Replies: 4
Views: 2,038
Posted By husamia
I am curious about your data and brings unrelated...

I am curious about your data and brings unrelated question? Aren't <20bp reads considered ambigous? Technically its possible that good amount of your reads align to multiple regions in genome. Hence...
Forum: Bioinformatics 07-14-2011, 04:43 AM
Replies: 366
Views: 198,487
Posted By husamia
The program is very efficient in memory usage to...

The program is very efficient in memory usage to make it run on any system. I have one concern for some applications that contain large number of sequence reads which require obviously larger system...
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