User: liangjiao.xue

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liangjiao.xue100
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Posts by liangjiao.xue

<prev • 12 results • page 1 of 2 • next >
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Answer: A: Download control cel files for specific tissue
... You may want to search the following database to get data from interested tissues of particular species. https://www.ebi.ac.uk/arrayexpress/ ...
written 2.5 years ago by liangjiao.xue100
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Comment: C: Comparison of Affymetrix with other platforms
... I think you could get the answers from the following aspects: 1) For most of the species, Affymetrix was usually among the platforms that gave solutions at the earliest time. 2) Prices were competitive. 3) Researchers prefer platforms with more users, to make their data easier to be compared with o ...
written 2.5 years ago by liangjiao.xue100
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Answer: A: transform RPM to TPM
... TPM, FPKM, RPKM are calculated from raw read counts. It will be easier to start from raw counts rather than to convert from different calculations. If RPM is "reads per million total/mapped reads", it's same as TPM (transcripts per million reads) for single-end platforms. For paired-end reads, s ...
written 2.5 years ago by liangjiao.xue100
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Answer: A: where to download blat command tool for windows?
... Just in case some people are looking for blat on Windows. Windows 10: https://github.com/liangjiaoxue/AGEseq/blob/master/blat_windows10.zip Before Windows 10 (tested on XP, 7, and 8) https://github.com/liangjiaoxue/AGEseq/blob/master/blat_windows.zip This version will make Windows 1 ...
written 2.5 years ago by liangjiao.xue100
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Answer: A: Inaccurate/Undesired results from bcftools version 1.1 convert --tsv2vcf command
... This is one late response. I think it is necessary because I spent hours to resolve this problem. Originally, I thought this is a very easy case to convert from MUMmer/snps to VCF. However, it not that easy to get the correct solution. Some traps: 1) You need to check the reference sequence t ...
written 2.9 years ago by liangjiao.xue100
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Comment: C: How to visualize large VCF files
... You could visualize VCF files in https://www.broadinstitute.org/igv/ The VCF can be zipped and indexed using tabix bgzip BIG.vcf tabix -p vcf BIG.vcf.gz ...
written 3.2 years ago by liangjiao.xue100
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Answer: A: Merging two libraries of amplicon
... If you search "paired end merge" you may get some information about software for this task. FLASh worked well in my case. ( http://ccb.jhu.edu/software/FLASH/ ). You could also try PEAR: http://sco.h-its.org/exelixis/web/software/pear/ Well, these two tools only merge paired reads in o ...
written 3.2 years ago by liangjiao.xue100
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Answer: A: WGCNA sequence of commands
... Yes. In this file, too few samples are included. No gene pass the QC filtering. ...
written 3.2 years ago by liangjiao.xue100
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Answer: A: Python script to trim 3' A nucleotides running slow
... Regular expression would be a good solution to avoid checking each nt. import re pattern = re.compile(r"A+$") # put this pattern out side of the loop with open(outfile, "w") as f: # avoid open files in the loop if not necessary for read in SeqIO.parse(infile, "fastq" ...
written 3.2 years ago by liangjiao.xue100
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Comment: C: How to convert relative coordinate to aboulate coordinate at genome?
... One GFF/GTF file is needed to get the positions and directions of genes on the genome. The input file shown here is very specific. I doubt there is some existing tool to convert the coordinate directly. Since R is tagged here, you could read the following link to load the GFF/GTF file into memory. ...
written 3.2 years ago by liangjiao.xue100

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