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Search: Posts Made By: Himalaya
Forum: Bioinformatics 12-25-2012, 12:48 AM
Replies: 1
Views: 1,434
Posted By Himalaya
Did you check a box "Active". In project click ...

Did you check a box "Active". In project click "Read Data" tab, you will find menus "name" "annotation" "group" and "active". Check the box and try it.
Forum: Bioinformatics 12-24-2012, 07:30 AM
Replies: 6
Views: 3,501
Posted By Himalaya
Please check the NGS QC toolkit paper...

Please check the NGS QC toolkit paper (http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030619). The QC steps are clear in it. Depending upon your sequence reads and trimming...
Forum: 454 Pyrosequencing 12-23-2012, 09:12 AM
Replies: 3
Views: 2,730
Posted By Himalaya
Cool, Will let you know about the tool. Sorry for...

Cool, Will let you know about the tool. Sorry for late reply. More update on the tool. Now the tool is also able to remove the sequencing errors or pcr error based on the codon space alignment and...
Forum: Bioinformatics 12-23-2012, 08:55 AM
Replies: 6
Views: 3,501
Posted By Himalaya
Carmen Sorry i don't get which parameter you...

Carmen
Sorry i don't get which parameter you saying about. It works so easy for me. If you input file has 454 short reads in fastq format, the command i posted earlier works easily for you as well....
Forum: 454 Pyrosequencing 11-12-2012, 10:23 PM
Replies: 3
Views: 2,730
Posted By Himalaya
Hi Mr Jefferson I am researching in HIV Drug...

Hi Mr Jefferson
I am researching in HIV Drug resistance mutations (DRM) in HIV quasispecies from infected patient to develop a tool for quick DRM detection. Initially I also tried to use AVA but...
Forum: 454 Pyrosequencing 10-22-2012, 09:25 AM
Replies: 0
Views: 1,825
Posted By Himalaya
Unhappy 454 Amplicon Variant Analyzer creating consensus sequence

Hi All
Do anyone know how Amplicon Variant Analyzer (AVA) make consensus sequence from individual aligned sequences?
Forum: Bioinformatics 08-22-2012, 05:53 AM
Replies: 28
Views: 7,847
Posted By Himalaya
Finally I got QTrim to quality trim the 454...

Finally I got QTrim to quality trim the 454 sequence reads. It also outputs the graphical plots showing the quality trend of reads before and after quality trimming. QTrim is available here...
Forum: 454 Pyrosequencing 08-22-2012, 05:49 AM
Replies: 3
Views: 1,542
Posted By Himalaya
Newbler trims the reads such that the cleaned...

Newbler trims the reads such that the cleaned reads have average quality score of 20 or above and yokoyang mentioned above, it only labels the cut point and really not trim the bases out of read. I...
Forum: 454 Pyrosequencing 08-22-2012, 05:44 AM
Replies: 2
Views: 3,664
Posted By Himalaya
I found another tool QTrim for quality trimming....

I found another tool QTrim for quality trimming. (hiv.sanbi.ac.za/software/qtrim)
Forum: Bioinformatics 08-22-2012, 02:39 AM
Replies: 6
Views: 3,501
Posted By Himalaya
Try QTrim (hiv.sanbi.ac.za/software/qtrim) It...

Try QTrim (hiv.sanbi.ac.za/software/qtrim)
It is python script and is commandline. It only does quality trimming and gives you the clean reads. No any vector trimming or adaptor trimming. Input...
Forum: 454 Pyrosequencing 01-11-2012, 07:08 AM
Replies: 5
Views: 8,972
Posted By Himalaya
Hi Maven ... Firstly, the precursor sff file...

Hi Maven ...
Firstly, the precursor sff file is split using sfffile tool, i think, so the files i got are sff file, not fasta file, after splitting using individual MID. Also the the trim point is...
Forum: 454 Pyrosequencing 01-10-2012, 11:53 PM
Replies: 5
Views: 8,972
Posted By Himalaya
Hi Vamosia I tried ignoring the MID section and...

Hi Vamosia
I tried ignoring the MID section and specified the primers and reference also. But still not working. Are you saying about sequencing data in sff containing no any MID sequence? We have a...
Forum: 454 Pyrosequencing 12-06-2011, 04:02 PM
Replies: 14
Views: 4,455
Posted By Himalaya
Hello I am also using Ava variant analyzer. The...

Hello
I am also using Ava variant analyzer. The software produces the consensus sequence but I would like to change the parameters for producing the consensus alignment. Do anyone know how to change...
Forum: 454 Pyrosequencing 11-16-2011, 07:13 AM
Replies: 2
Views: 3,664
Posted By Himalaya
Unhappy newbler quality trimming

Hi All
Does anyone has tried to do the quality trimming of 454 short sequence reads? My 454 short sequence reads are already trimmed for adaptors and MIDs. But there are poor quality bases that I...
Forum: Bioinformatics 11-16-2011, 07:10 AM
Replies: 5
Views: 3,111
Posted By Himalaya
newbler quality trimming

Hi All
Does anyone has tried to do the quality trimming of 454 short sequence reads? My 454 short sequence reads are already trimmed for adaptors and MIDs. But there are poor quality bases that I...
Forum: Bioinformatics 10-08-2011, 10:32 PM
Replies: 35
Views: 12,806
Posted By Himalaya
Firstly, I did not use human sized genome. I was...

Firstly, I did not use human sized genome. I was doing metagenomics assembly of three known bacterial genome. Secondly, my computing time varied as I was not only the one using the HPC. If you are...
Forum: Bioinformatics 10-08-2011, 03:29 AM
Replies: 35
Views: 12,806
Posted By Himalaya
I did a small comparative study of soap denovo,...

I did a small comparative study of soap denovo, velvet, ABYSS and cortex. I could not use allpaths. SOAP devono is fast than other but uses very huge memory. ABYSS does better assembly but velvet is...
Forum: Bioinformatics 06-27-2011, 06:08 AM
Replies: 28
Views: 7,847
Posted By Himalaya
HI Rob Can you show me where can i find the...

HI Rob
Can you show me where can i find the working principle of prinseq? I would like to know how prinseq trims off the low quality score bases?
Forum: Bioinformatics 06-26-2011, 02:30 AM
Replies: 28
Views: 7,847
Posted By Himalaya
hi essvee Do you know how seqtrim cleans up the...

hi essvee
Do you know how seqtrim cleans up the low quality bases. I mean the actual steps or methodology? My sequences are already clean from primers and adaptors. I just need to clean low quality...
Forum: Bioinformatics 06-10-2011, 05:36 AM
Replies: 28
Views: 7,847
Posted By Himalaya
Hi Jose Its fine now. The command is working....

Hi Jose
Its fine now. The command is working. But I have a question. If I want to cleaning minimum threshold quality score, how can i do that? Since --qual_threshold does not work for 454, how is...
Forum: Bioinformatics 06-09-2011, 06:59 AM
Replies: 28
Views: 7,847
Posted By Himalaya
Hi Jose I am going with your explainations. I...

Hi Jose
I am going with your explainations. I issued the followed command:
clean_reads -i Pair01_fastq_format.fastq -o ./clean_reads/output_q20_len_50 -p 454 -f fastq -g fastq -min_length 20...
Forum: Bioinformatics 06-09-2011, 05:54 AM
Replies: 28
Views: 7,847
Posted By Himalaya
Hi Jose I am trying to do quality trimming and...

Hi Jose
I am trying to do quality trimming and filtering 454 reads. The adaptors and primers and barcode sequences are already removed.I am not allowed to specific minimum quality threshold to clean...
Forum: Bioinformatics 06-08-2011, 05:59 AM
Replies: 28
Views: 7,847
Posted By Himalaya
Hi Jose, Thanks a lot. In linux it seems to work...

Hi Jose, Thanks a lot. In linux it seems to work now..For the same command again, it gives me output " parameter qual_threshold is incompatible with platform long_with_quality". I tested the...
Forum: Bioinformatics 06-08-2011, 04:30 AM
Replies: 28
Views: 7,847
Posted By Himalaya
Hi Jose I am using mac os snow leopard. My...

Hi Jose
I am using mac os snow leopard. My commandline is: clean_reads -i Pair01.fastq -o ./clean_reads/output_q20_len50_only3end -p 454 -f fastq -g fastq -qual_threshold 20 -only_3_end True...
Forum: Bioinformatics 06-08-2011, 03:39 AM
Replies: 28
Views: 7,847
Posted By Himalaya
Hi Jose Blanca..I installed clean_reads with...

Hi Jose Blanca..I installed clean_reads with Biopython and psubprocess preinstalled according to requirement but resulted to segmentation fault. have you run the program? Please advice me about the...
Showing results 1 to 25 of 38

 


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