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Search: Posts Made By: yksikaksi
Forum: Bioinformatics 03-21-2017, 01:02 AM
Replies: 12
Views: 30,205
Posted By yksikaksi
Please give more information about the data...

Please give more information about the data above. A brief summary of your method and work will be hlepful for those who might able to help.
Forum: Bioinformatics 09-14-2012, 06:07 AM
Replies: 22
Views: 4,821
Posted By yksikaksi
Do you have experience to work with the non model...

Do you have experience to work with the non model species onCytoscape? I have RNA-Seq data of non model species and I would like to do the biological pathway analysis, Cytoscape came to my mind as I...
Forum: Bioinformatics 07-10-2012, 04:54 AM
Replies: 1
Views: 1,496
Posted By yksikaksi
Question SHRiMP2 mapping report

Pairs Matched: 9,371 (35.4532%) <--
... with QV >= 10: 2,351 (8.8945%)
Pairs Dropped: 0 (0.0000%)
...
Forum: SOLiD 06-19-2012, 06:07 AM
Replies: 36
Sticky: SOLiD Adapters
Views: 44,880
Posted By yksikaksi
Dear dongyongdong, Perhaps you could have a...

Dear dongyongdong,

Perhaps you could have a look on this post (http://seqanswers.com/forums/showpost.php?p=1681&postcount=2) of this thread.
Forum: Bioinformatics 05-06-2012, 11:49 PM
Replies: 5
Views: 5,179
Posted By yksikaksi
Thanks swbarnes2 for your suggestion. :)

Thanks swbarnes2 for your suggestion. :)
Forum: Bioinformatics 05-02-2012, 10:39 PM
Replies: 5
Views: 5,179
Posted By yksikaksi
Thanks guys for your input. It is a bit...

Thanks guys for your input.

It is a bit strange I don't receive feedback alert email from the forum.

Maybe I should rephrase my question. Put it in this way, I want to filter the genes (tags)...
Forum: Bioinformatics 05-01-2012, 02:33 AM
Replies: 5
Views: 5,179
Posted By yksikaksi
Question Exclude certain tags from BAM file

Wishing you guys have a nice Mayday.

I want to exclude certain reference tags(genes) from BAM files and direct the output to a new BAM file. I tired with SAMtools commend as below:

foreach...
Forum: Bioinformatics 04-26-2012, 11:24 AM
Replies: 5
Views: 2,359
Posted By yksikaksi
Thanks for the code and the explanation. Thanks a...

Thanks for the code and the explanation. Thanks a lot.
Forum: Bioinformatics 04-25-2012, 11:02 PM
Replies: 5
Views: 2,359
Posted By yksikaksi
I want to exclude unmapped reads from the PCR...

I want to exclude unmapped reads from the PCR duplicates removed BAM file (done by Picard MarkDuplicates tools) before carry on to downstream analysis. Thanks for the replied and suggestions....
Forum: Bioinformatics 04-24-2012, 11:21 PM
Replies: 5
Views: 2,359
Posted By yksikaksi
Question How can I parse these reads

::::::::::::::
0H.ptFlagstat.txt
::::::::::::::
49080460 + 0 in total
0 + 0 duplicates
6444347 + 0 mapped (13.13%:nan%)
49080460 + 0 paired in sequencing
45547041 + 0 read1
3533419 + 0...
Forum: SOLiD 04-19-2012, 12:47 AM
Replies: 4
Views: 2,513
Posted By yksikaksi
Thanks, kopi-o. I'm doing RNA-seq analysis...

Thanks, kopi-o.

I'm doing RNA-seq analysis with SOLiD platform. I read people mentioned carry out quality filtering (someone also called it as pre-filtering) before mapping is recommended....
Forum: SOLiD 04-19-2012, 12:12 AM
Replies: 4
Views: 2,513
Posted By yksikaksi
Sorry for the unclear question. The...

Sorry for the unclear question.

The pre-filtering I refer here is view the reads with tools for example FastQC or Fastx and then trim out the so-called bad bases before mapping the reads.

The...
Forum: SOLiD 04-18-2012, 05:55 AM
Replies: 4
Views: 2,513
Posted By yksikaksi
Question What is the differences between pre-filtering vs PCR duplicates remove mapped reads?

Hello,

Does is a must to preform pre-filtering for color space reads before mapping?

Could it has a big differences in downstream analysis when I mapped the SOLiD color space reads without...
Forum: SOLiD 04-18-2012, 04:29 AM
Replies: 22
Views: 5,991
Posted By yksikaksi
Hum... it is strange. I managed to map my csfasta...

Hum... it is strange. I managed to map my csfasta reads with SHRiMP2 but not BWA.
Forum: SOLiD 04-18-2012, 12:07 AM
Replies: 22
Views: 5,991
Posted By yksikaksi
Have you consider to map your csfasta reads with...

Have you consider to map your csfasta reads with SHRiMP2?
Forum: Bioinformatics 11-06-2011, 09:18 PM
Replies: 2
Views: 3,574
Posted By yksikaksi
Thanks Richard Finney. I came across to...

Thanks Richard Finney.

I came across to this piece of modified solid2fastq.pl script by bgulko (http://seqanswers.com/forums/showpost.php?p=16590&postcount=17) in bwa color-space index...
Forum: Bioinformatics 11-06-2011, 06:53 AM
Replies: 2
Views: 3,574
Posted By yksikaksi
Question Unmatched read name error when converting csfasta to fastq with solid2fastq.pl

I'm encountered with "unmatched read name" error when I converting paired SOLiD csfasta files to fastq by using solid2fastq.pl from bwa-0.5.9

The error message:
================================...
Forum: Bioinformatics 10-30-2011, 09:36 PM
Replies: 2
Views: 4,695
Posted By yksikaksi
I see. Thanks for the information.

I see. Thanks for the information.
Forum: Bioinformatics 10-30-2011, 09:43 AM
Replies: 2
Views: 4,695
Posted By yksikaksi
Unhappy Convert csfasta to fastq

Good day.

I would like to know is there a must to include .qual file while converting the SOLiD .csfasta file format to .fastq file format for BWA alignment? I plan to use solid2fastq.pl to do...
Forum: SOLiD 11-30-2010, 01:49 AM
Replies: 36
Sticky: SOLiD Adapters
Views: 44,880
Posted By yksikaksi
You can refer to this appendix D...

You can refer to this appendix D (http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_081746.pdf) (page 206 onwards) of Applied Biosystems SOLiD™ 4 System Library...
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