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Forum: Bioinformatics 04-19-2013, 02:46 AM
Replies: 0
Views: 836
Posted By mingkunli
wired error profile

Hi,

We are using MiSeq to sequence a 350bp PCR fragment (250bp paired-end, multiplex with 100 samples, using dual indexes), since this is PCR prodect, we diluted the library 1:10 to get a better...
Forum: Bioinformatics 06-08-2011, 09:01 AM
Replies: 1
Views: 2,505
Posted By mingkunli
Any scripts converting fastq 2 scarf

Since Splinter(new version of snp-seeker) use scarf as the input, I need something that could convert my fastq file to scarf file, anyone know some? thanks.
Forum: Illumina/Solexa 11-10-2010, 01:58 AM
Replies: 3
Views: 1,819
Posted By mingkunli
Thanks for your reply, I still need them, but...

Thanks for your reply, I still need them, but why these reads have such high quality score ("h" for most of the time)?
Forum: Illumina/Solexa 10-14-2010, 11:52 AM
Replies: 3
Views: 1,819
Posted By mingkunli
Phix174 solexa reads repository

I need phix174 solexa data to do some test (the control DNA provided by ILLumina), any one know where I can find some?

Thanks.
Forum: Bioinformatics 08-06-2010, 10:22 AM
Replies: 30
Views: 52,667
Posted By mingkunli
now I come to anther question: once we have reads...

now I come to anther question: once we have reads with various lengths, should 3' coordinates should also be considerred(or length of the aligned part) ? for reads from the reverse strand, 3' is the...
Forum: Illumina/Solexa 04-25-2010, 01:26 AM
Replies: 3
Views: 1,604
Posted By mingkunli
Thanks, seems it's not there.

Thanks, seems it's not there.
Forum: Illumina/Solexa 04-16-2010, 02:12 AM
Replies: 3
Views: 1,604
Posted By mingkunli
Do you think it's sequencing error?

TAT-TTTCGTCTG
TATCTTTCGTTTG


These two kinds of reads appear several times, also TAT-TTTCGTTTG.
I know it's likely to be sequencing error for 454 data, but I don't know any mechanism can be...
Forum: Bioinformatics 04-06-2010, 08:32 AM
Replies: 0
Views: 2,222
Posted By mingkunli
circular genome assembling

Now I copy the first 75bp(if I have 76 long read) to the end of the sequence. However I found it's hard to sum up the mapping info for this regions(have to combine the info from two regions). Is...
Forum: Bioinformatics 03-26-2010, 08:09 AM
Replies: 2
Views: 1,678
Posted By mingkunli
Thanks, lh3. if I want to use -F to filter...

Thanks, lh3.

if I want to use -F to filter out two Flags, or -f to keep two Flags, should I use -F 48, otherwise, I can run -F 4, and -F 8 separately.

I met the flag 87 with my pair-end data...
Forum: Bioinformatics 03-25-2010, 04:02 AM
Replies: 2
Views: 1,678
Posted By mingkunli
PE data processed by bwa

I am processing the PE solexa data using BWA, I met a problem after I looked through the sampe result.

Although I set the -a(maximum insert size) to be 300, I still found lots of PE mapped with...
Forum: Illumina/Solexa 01-27-2010, 12:35 PM
Replies: 5
Views: 9,113
Posted By mingkunli
That's exact what we found, 1301, with equivalent...

That's exact what we found, 1301, with equivalent amount of A and G.
Actually, I am using this data to test my method to detect heteroplasmy, however, I am not sure whether the Phix data is clean.
Forum: Illumina/Solexa 01-20-2010, 04:07 PM
Replies: 5
Views: 9,113
Posted By mingkunli
I used that data based on one assumption: only...

I used that data based on one assumption: only one genome there, I wonder to what extent it is true.
Forum: Illumina/Solexa 01-20-2010, 03:51 PM
Replies: 5
Views: 9,113
Posted By mingkunli
I found actually there are some SNP have been...

I found actually there are some SNP have been found, But if it's possible to have two different phix genome in the control lane? which will influence the concensus calling rather than sequencing...
Forum: Illumina/Solexa 01-20-2010, 03:34 PM
Replies: 5
Views: 9,113
Posted By mingkunli
what's in solexa's control lane

I have been told that the phix genome used in solexa's control lane should be free of SNP, which means the reads should be exactly mapped to the phix genome if there is no sequencing eror, but as far...
Forum: Bioinformatics 11-09-2009, 07:08 AM
Replies: 10
Views: 6,942
Posted By mingkunli
btw, how did you covert 454 reads to fastq format?

btw, how did you covert 454 reads to fastq format?
Forum: Bioinformatics 11-09-2009, 06:50 AM
Replies: 6
Views: 15,073
Posted By mingkunli
Where these words come from? I can't understand...

Where these words come from?
I can't understand if (p->n_mm == mm) return 25;

and for my data,
XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 gives a quality score 25,
XT:A:U NM:i:0 ...
Forum: Bioinformatics 10-24-2009, 09:02 AM
Replies: 0
Views: 1,174
Posted By mingkunli
how to get the final consensus by samtool

using samtools -c, I can retrieve the consensus sequence without indel(from column 4).
using samtools -cf, although indel info is included, but seems no way to retrieve the final consensus, since...
Forum: Bioinformatics 09-08-2009, 05:30 AM
Replies: 5
Views: 13,002
Posted By mingkunli
hey Jing, thanks for your help. I also got the...

hey Jing, thanks for your help.
I also got the reply from the author, thanks to lh3
1) Both optimal and suboptimal hits are stored in .sai files, but only
approximate chromosomal positions are...
Forum: Bioinformatics 09-08-2009, 02:20 AM
Replies: 5
Views: 13,002
Posted By mingkunli
what's in bwa's .sai file

besides the content that shown in .sam file(alignment of the best match, and number of suboptimal/all hits), seems it also contains some information of the suboptimal hits, is it possible to look at...
Forum: Bioinformatics 09-05-2009, 09:06 AM
Replies: 2
Views: 2,038
Posted By mingkunli
:) Thanks for reminding me of the -e option. I...

:)
Thanks for reminding me of the -e option. I will try your BFAST if longer than 10bp indels are expected in my reads.
Forum: Bioinformatics 09-04-2009, 06:28 AM
Replies: 2
Views: 2,038
Posted By mingkunli
output all possible match using bwa

I am moving from bowtie to bwa, as bwa considers gap while doing mapping.
But i don't know how to get all the possible hits for a single read on the reference genome(besides the perfect one), like...
Forum: Illumina/Solexa 08-28-2009, 08:15 AM
Replies: 0
Views: 3,819
Posted By mingkunli
repetitive sequence

finally I have to deal with the repetitive sequence or the so-called paralog seqence when I do the assembling. I did simulation, found it would change my consensus sequence and of course influence...
Forum: Illumina/Solexa 04-24-2009, 08:12 AM
Replies: 13
Views: 2,732
Posted By mingkunli
I don't do wet work. What I can tell you is they...

I don't do wet work. What I can tell you is they tried lots of primers, and most of them don't work, even works, only on some individuals.
concerning the barcoding, we use the protocol published on...
Forum: Illumina/Solexa 03-19-2009, 08:47 AM
Replies: 3
Views: 2,254
Posted By mingkunli
Hey Bach, Thanks for your response, we plan to go...

Hey Bach, Thanks for your response, we plan to go deep into the sequence error, hope can get more general ideas.

now we get too much AC misidentification, and seems they cluster into several...
Forum: Illumina/Solexa 03-19-2009, 07:14 AM
Replies: 3
Views: 2,254
Posted By mingkunli
context-dependent sequence error

Have you ever read such report? seems I found some sequence error hotspots.
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