User: sunhanice

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sunhanice190
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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 2.1 years ago by sunhanice190
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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 2.4 years ago by sunhanice190
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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 2.5 years ago by sunhanice190
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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 2.5 years ago by sunhanice190
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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 2.6 years ago by sunhanice190
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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 2.6 years ago by sunhanice190
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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 2.7 years ago by sunhanice190
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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 2.7 years ago by sunhanice190
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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 2.7 years ago by sunhanice190
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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 3.0 years ago by sunhanice190

Latest awards to sunhanice

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?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How Many Cells Will Be Involved In One Dna Or Rna Sequencing?
Teacher 2.4 years 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 2.4 years ago, voted at least 25 times.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Substitution Per Mb

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