Forum: Bioinformatics
12-25-2012, 12:48 AM
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Replies: 1
Views: 1,434
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Forum: Bioinformatics
12-24-2012, 07:30 AM
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Replies: 6
Views: 3,501
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...
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Forum: 454 Pyrosequencing
12-23-2012, 09:12 AM
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Replies: 3
Views: 2,730
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Forum: Bioinformatics
12-23-2012, 08:55 AM
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Replies: 6
Views: 3,501
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....
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Forum: 454 Pyrosequencing
11-12-2012, 10:23 PM
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Replies: 3
Views: 2,730
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...
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Forum: 454 Pyrosequencing
10-22-2012, 09:25 AM
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Replies: 0
Views: 1,825
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Forum: Bioinformatics
08-22-2012, 05:53 AM
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Replies: 28
Views: 7,847
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...
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Forum: 454 Pyrosequencing
08-22-2012, 05:49 AM
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Replies: 3
Views: 1,542
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...
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Forum: 454 Pyrosequencing
08-22-2012, 05:44 AM
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Replies: 2
Views: 3,664
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Forum: Bioinformatics
08-22-2012, 02:39 AM
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Replies: 6
Views: 3,501
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...
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Forum: 454 Pyrosequencing
01-11-2012, 07:08 AM
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Replies: 5
Views: 8,972
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...
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Forum: 454 Pyrosequencing
01-10-2012, 11:53 PM
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Replies: 5
Views: 8,972
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...
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Forum: 454 Pyrosequencing
12-06-2011, 04:02 PM
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Replies: 14
Views: 4,455
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...
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Forum: 454 Pyrosequencing
11-16-2011, 07:13 AM
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Replies: 2
Views: 3,664
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...
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Forum: Bioinformatics
11-16-2011, 07:10 AM
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Replies: 5
Views: 3,111
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...
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Forum: Bioinformatics
10-08-2011, 10:32 PM
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Replies: 35
Views: 12,806
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Forum: Bioinformatics
10-08-2011, 03:29 AM
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Replies: 35
Views: 12,806
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...
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Forum: Bioinformatics
06-27-2011, 06:08 AM
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Replies: 28
Views: 7,847
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Forum: Bioinformatics
06-26-2011, 02:30 AM
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Replies: 28
Views: 7,847
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...
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Forum: Bioinformatics
06-10-2011, 05:36 AM
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Replies: 28
Views: 7,847
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...
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Forum: Bioinformatics
06-09-2011, 06:59 AM
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Replies: 28
Views: 7,847
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...
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Forum: Bioinformatics
06-09-2011, 05:54 AM
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Replies: 28
Views: 7,847
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...
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Forum: Bioinformatics
06-08-2011, 05:59 AM
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Replies: 28
Views: 7,847
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Forum: Bioinformatics
06-08-2011, 04:30 AM
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Replies: 28
Views: 7,847
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...
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Forum: Bioinformatics
06-08-2011, 03:39 AM
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Replies: 28
Views: 7,847
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...
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