User: litiancheng.gansu

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Posts by litiancheng.gansu

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Why Pair Ends Data'S Ecah Pair'S Alignment Statistic And The Sum Of Them Are Dif
... Yes, I think you are right. I rechecked another sample, which the difference between standalone end's alignment statistics and Pair Ends's end alignment statistics are small, they are nearly same(like the above example's Read1's case), this is because the Read2(above example)'s quality is so bad tha ...
written 5.6 years ago by litiancheng.gansu10
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Why Pair Ends Data'S Ecah Pair'S Alignment Statistic And The Sum Of Them Are Different
... I have a sample's data, using illumina 's Piar End sequencing technology. RE19E2T40PA_L1_I040.pairPrimer_1.fastq (Read1) RE19E2T40PA_L1_I040.pairPrimer_2.fastq (Read2) I have aligned both Read1 and Read2 to hg19 using BWA, and generated three bam file. RE19E2T40PA_L1_I040.pairPrimer_1.fastq ...
paired-end picard bwa written 5.6 years ago by litiancheng.gansu10 • updated 5.6 years ago by swbarnes24.6k
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Answer: A: Svdetect-Structure And Cnv Detection
... What type of your data is, if it is Mate pair reads, the mu_length shouldn't be so small, in this case, it maybe your library which contain lots of PE data which should not be existed in you Mate Pair data. With a so small window size, there would be too many genome fragments, of course, more time a ...
written 5.7 years ago by litiancheng.gansu10
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How To Detect And Remove Loxp Sequence Form Mate Pair Reads
... I have some mate pair data to analysis, could any one give me some suggestion about how to detect and remove loxp sequence in the mate pair reads. I have found the R script: DeLoxer which seems could do my job, but I tested it and it eat all of my server memory, what more, it's performance is so ba ...
written 5.8 years ago by litiancheng.gansu10
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Comment: C: Get Special Mutation Site'S Special Allele Reads
... Yes, with your help, I 'm almost there, I can write some scripts to check the special site's base to determine whether to report that read, but that would make me to spend lots of time, if there were some tools that could do this would be better. ...
written 6.0 years ago by litiancheng.gansu10
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Get Special Mutation Site'S Special Allele Reads
... I have done GATK's UnifiedGenotyper and get some variations, One of these variations is really the one I'm interested in, that's a T>G mutation(T is the reference base, G is the query reads base), T:6890, while G gets 162. I want to get the 162 reads with G on the mutation site, how can I done t ...
gatk written 6.0 years ago by litiancheng.gansu10 • updated 3.1 years ago by Biostar ♦♦ 20
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What Bio::Factory Is In Bioperl
... I'm studying bioperl recently, but I don't know factory in bioperl, what does it do? could anyone help me to understand it? ...
bioperl written 6.0 years ago by litiancheng.gansu10 • updated 6.0 years ago by Neilfws48k
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Comment: C: Create Consensus Sequences For Sequence Pairs Within A Multiple Alignment?
... hi, Steve Moss, I cant not connect to that link, could you please send me that script, thank you! ...
written 6.1 years ago by litiancheng.gansu10
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Comment: C: How To Determine The Location Of A Peak In A List Of Numbers
... thanks, I found I had described the issue incompletely, there are two or more peaks in my data. ...
written 6.1 years ago by litiancheng.gansu10
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Comment: C: Merge Paired-End Reads
... It's no available, the web page cannot be open. http://genomics.jhu.edu/software/FLASH/index.shtml ...
written 6.1 years ago by litiancheng.gansu10

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