User: sunhanice

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sunhanice180
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9 months ago
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Posts by sunhanice

<prev • 18 results • page 1 of 2 • next >
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Answer: A: How to remove reads associated with a specific region from bam file?
... Just found, there is an option -U in samtools view. Use it like this: samtools view input.bam -b -h -o output_inRegions.bam -U output_outRegions.bam -L Regions.bed ...
written 16 months ago by sunhanice180
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Answer: A: free/cheap bioinformatics web application hosting
... Have you tried the official free recommendations, such as Heroku or dotCloud?  I am not sure whether other programs are allowed to install. Another option is a VPS, although it will cost a bit. I would like recommend ramnode. ...
written 20 months ago by sunhanice180
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Comment: C: Why there are some genes have a same transcription start position?
... where is the second picture? different genes have same txStart on the same strand? ...
written 21 months ago by sunhanice180
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Answer: A: editing count.py script of HTSeq to work with bed file
... Agree with Istvan, it is easier to convert bed to gtf instead of changing the source code.  Please refer to this post, https://www.biostars.org/p/103263/ make sure the gtf file has 9 columns like the following,  scaffold00001    UNCC    exon    488375    489180    .    -    0    gene_id "101_g"; ...
written 21 months ago by sunhanice180
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Answer: A: dispersion of a gene, what does it mean?
... In my understanding, you can. From the definition of dispersion, In statistics, dispersion (also called variability, scatter, or spread) denotes how stretched or squeezed a distribution (theoretical or that underlying a statistical sample) is. Common examples of measures of statistical dispersion a ...
written 22 months ago by sunhanice180
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Answer: A: Between mm10.p4 and mm10, why the total sequence length different?
... From my understanding, total number of nucleotides may be different. But, the number of nucleotides on the major chromosomes (chr1, chr2, ..., chrX, chrY) should be kept the same for the same version reference. ...
written 22 months ago by sunhanice180
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Comment: C: SNP position in sample sequences
... Each line has one position. Some samples at this position have SNP (0/1, 1/1), and some samples not (0/0). ...
written 23 months ago by sunhanice180
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Answer: A: SNP position in sample sequences
... There should be several columns after FORMAT column, each containing one sample.  For example, in this line of vcf: 5       11956   snp_5_11956     G       C       100.00  PASS    AA=.;AC=56;AF=0.03;AFR_AF=0.11;AMR_AF=0.01;AN=2184;AVGPOST=0.9907;DAF_GLOBAL=.;ERATE=0.0005;GERP=.;LDAF=0.0273;RSQ=0.8 ...
written 23 months ago by sunhanice180
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Answer: A: How can I change the default path to which SRA files are downloaded?
... I always downloaded SRA files directly using wget, and then converted them to fastq.tar.gz locally with fastq-dump. The file address for SRA file is like this format: /sra/sra-instant/reads/ByRun/sra/{SRR|ERR|DRR}/<first 6 characters of accession>/<accession>/<accession>.sra For ...
written 24 months ago by sunhanice180
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Answer: A: blastn use help
... Have you already indexed your database before the searching using the command like this? makeblastdb -dbtype nucl -in input.fasta ...
written 2.3 years ago by sunhanice180

Latest awards to sunhanice

Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How can I change the default path to which SRA files are downloaded?
Popular Question 16 months ago, created a question with more than 1,000 views. For How Many Cells Will Be Involved In One Dna Or Rna Sequencing?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: How can I change the default path to which SRA files are downloaded?
Supporter 20 months ago, voted at least 25 times.
Popular Question 21 months ago, created a question with more than 1,000 views. For Substitution Per Mb

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