User: sckinta

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sckinta450
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Posts by sckinta

<prev • 45 results • page 1 of 5 • next >
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Inconsistency on ensemble transcript id between ucsc and gencode
... I want to classify the peaks/regions I identified from my sequencing experiment to certain annotated regions (intron, 3UTR, CDS, exon and intergenic region) in genome build hg19. So i downloaded some annotation files from both ucsc and gencode. Using ucsc table browser, I selected genome build GRC ...
genome assembly written 11 days ago by sckinta450
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Comment: C: How to create a faster way to match a list of string to a list of patterns in r?
... I tried to use separate(sample, c('description','id','Source_Name'), sep="\\.") to get the last part of pattern, however, since the sample str (string_list) is messy, it causes warnings. I went to manually solve it. but I am looking for an automatic way to do this. ...
written 19 days ago by sckinta450
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Comment: C: How to create a faster way to match a list of string to a list of patterns in r?
... [pattern_list.txt][1] list [string_list.txt][2] [1]: http://ucsctrackhub.research.chop.edu/ucsc/sfgi/suc1/tmp/pattern_list.txt [2]: http://ucsctrackhub.research.chop.edu/ucsc/sfgi/suc1/tmp/string_list.txt ...
written 19 days ago by sckinta450
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How to create a faster way to match a list of string to a list of patterns in r?
... As the title, I have a list of strings (> 10,000). For each in string list, I want to know whether it can match any pattern in my pattern list (>10,000). The way I came up with is. # CREATE FUNC TO DETECT MATCH FOR EACH STR any_match <- function(str) { any(sapply(pattern_list ...
R string written 19 days ago by sckinta450 • updated 19 days ago by Michael Dondrup44k
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Comment: C: bcl2fastq report the whole sequences without trimming index and adaptor
... I am not sure that is the issue. We prepared the library and sequenced them in house. We demultiplexed successfully using the same index sequence direction setting on some other runs. I just recently changed the library prep kit from illumina kit to this Takara SMARTer® Stranded RNA-Seq Kit (with sw ...
written 25 days ago by sckinta450
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Comment: C: bcl2fastq report the whole sequences without trimming index and adaptor
... Yes, I tried that and be able to extract index for each read. However, after parsing the index sequence with customerized code, only 29% of reads can be assigned to library. ...
written 25 days ago by sckinta450
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Comment: C: bcl2fastq report the whole sequences without trimming index and adaptor
... Yeah, after checking the illumina sequence steps, I started to get that bcl2fastq does not trim data. Each cycle corresponds to each position in either read or index. In each cycle, read 1 was sequenced first (with 51 cycles in our case), then index i7 (with 8 cycles), then index i5 (8 cycles) and f ...
written 25 days ago by sckinta450
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bcl2fastq report the whole sequences without trimming index and adaptor
... We used bcl2fastq (v2.20.0.422) to convert pair-end RNAseq image file to fastq file. When preparing the sequencer, we set both read length 51 and dual index length 8 (see part of RunInfo.xml below) ...
next-gen sequencing written 26 days ago by sckinta450 • updated 26 days ago by drkennetz260
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Does IDR (irreproducible discovery rate) higher mean less 'reproducible' or vice versa?
... Applying [idr package][1] to ChIP-seq peaks allows researchers to compare multiple replicates and evaluate each peaks with reproducibility. It produces a output file which mimics the input narrowPeak file with additional two columns stating localIDR and globalIDR. Both localIDR and globalIDR represe ...
idr chip-seq written 5 months ago by sckinta450 • updated 4 weeks ago by goodez240
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what does allele frequency changes mean through multiple pairwise comparisons?
... I have three population to compare their allele frequency. Based on the previous AFLP fingerprint, we know B is derived from A. A and B are closer to each other compared to C, but B shows different phenotype from A and C.  We did RNAseq on those three populations and identified the differential exp ...
allele frequency written 2.6 years ago by sckinta450

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Popular Question 9 weeks ago, created a question with more than 1,000 views. For how to add/update node id to a tree in Bio::Tree::Tree object
Popular Question 5 months ago, created a question with more than 1,000 views. For Converting vcf to pileup
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Epic Question 21 months ago, created a question with more than 10,000 views. For Fastqc Over-Represented Sequences Are Adapters ?
Popular Question 21 months ago, created a question with more than 1,000 views. For Converting vcf to pileup
Popular Question 21 months ago, created a question with more than 1,000 views. For how to remove adaptor sequence which has more than 1 indexing barcode?
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Popular Question 21 months ago, created a question with more than 1,000 views. For Fastqc Over-Represented Sequences Are Adapters ?
Great Question 2.5 years ago, created a question with more than 5,000 views. For Fastqc Over-Represented Sequences Are Adapters ?
Epic Question 2.5 years ago, created a question with more than 10,000 views. For Why Does Rna-Seq Read Count Fit Poisson Distribution?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Fastqc Over-Represented Sequences Are Adapters ?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Fastx Invalid Quality Score Value
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Great Question 2.9 years ago, created a question with more than 5,000 views. For Fastqc Over-Represented Sequences Are Adapters ?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Fastx Invalid Quality Score Value
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Popular Question 3.9 years ago, created a question with more than 1,000 views. For Fastx Invalid Quality Score Value
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