User: grant.hovhannisyan

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Posts by grant.hovhannisyan

<prev • 176 results • page 1 of 18 • next >
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Answer: A: sratoolkit and download
... Try to install aspera utility https://www.ncbi.nlm.nih.gov/books/NBK158899/#SRA_download.accessing_the__ascp_utility, then prefetch the sra file (in my experience prefetch is more stable than fastq-dump), and once it is downloaded use fastq-dump. EDIT: Also you can try to find that dataset in ENA d ...
written 7 days ago by grant.hovhannisyan880
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Comment: C: Can I determine the machine used for RNA-seq from the .count file extension?
... Well, I said "usually" :) and the answer to the original question should be just "NO", but it wouldn't have helped much the OP. ...
written 11 days ago by grant.hovhannisyan880
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Answer: A: Can I determine the machine used for RNA-seq from the .count file extension?
... I am not sure if it is possible to do with count files. Usually the machine info can be found in [fastq file][1], so you might try to find the raw data and have a look. On the other hand, you can ask the people who has generated the data. [1]: https://en.wikipedia.org/wiki/FASTQ_format ...
written 12 days ago by grant.hovhannisyan880
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Comment: C: finding mutations in rna-seq transcriptome
... Convert is not a correct word here:) You need to map the reads (fastq file) to the reference genome (or transcriptome), if available, to obtain the bam file. To do it you can use for example STAR or Hisat2 software. ...
written 13 days ago by grant.hovhannisyan880
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Answer: A: finding mutations in rna-seq transcriptome
... As already mentioned, you can use GATK. But variant calling based on RNAseq data has its tricks, so better follow [the best practices of GATK specifically for RNAseq.][1] [1]: https://gatkforums.broadinstitute.org/gatk/discussion/3892/the-gatk-best-practices-for-variant-calling-on-rnaseq-in-full ...
written 13 days ago by grant.hovhannisyan880
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Comment: C: LEADING and TRAILING in TRIMMOMATIC
... Thanks, now it make sense to me. ...
written 20 days ago by grant.hovhannisyan880
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LEADING and TRAILING in TRIMMOMATIC
... Hi Biostars, I have been using trimmomatic for quite some time, but realized that I don't get something. So one can use LEADING and TRAILING options to remove bases from the beginning and end of the read, respectively. From manual: LEADING Remove low quality bases from the beginning. As long as a ...
trimmomatic rna-seq written 20 days ago by grant.hovhannisyan880 • updated 20 days ago by YaGalbi1.3k
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Answer: A: wget and download
... These posts answer your question https://www.biostars.org/p/111040/ https://www.biostars.org/p/209950/#314274 ...
written 26 days ago by grant.hovhannisyan880
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Comment: C: Which HTSeq mode is suitable for RNAseq data to be used for differential gene ex
... If you use STAR as mapper, you can specify the option `--quantMode GeneCounts` and STAR will output read counts equivalent to `htseq --union` option. Thus you can skip counting step in your pipeline and save time. ...
written 28 days ago by grant.hovhannisyan880
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Comment: C: download from SRA
... As far as I know, sra can block the ip if you download a lot of files with wget. ...
written 5 weeks ago by grant.hovhannisyan880

Latest awards to grant.hovhannisyan

Scholar 12 days ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Teacher 12 days ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Commentator 13 days ago, created a comment with at least 3 up-votes. For C: gatk tool installation problem
Popular Question 28 days ago, created a question with more than 1,000 views. For Read counts of STAR with gff file
Scholar 12 weeks ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: gatk tool installation problem
Teacher 3 months ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Scholar 3 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Scholar 3 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Teacher 3 months ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
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Scholar 4 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
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Scholar 9 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Teacher 9 months ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: gatk tool installation problem
Scholar 11 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO

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