User: ashish

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ashish200
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Posts by ashish

<prev • 92 results • page 1 of 10 • next >
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Comment: C: Downloading HMM profiles from Interpro
... Do you want all the HMM profiles or some selected ones? Anyways, if you don't find them then you can download PSSMs from [NCBI CDD][1] and then use them to perform RPS-BLAST against your sequences. [1]: ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/cdd.tar.gz ...
written 5 months ago by ashish200
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Comment: C: BLAST Command Line - restarting
... You need to add to the PATH variable not in comSpec. You have blast folder mention in your PATH variable but its not complete. use `C:\Program Files\NCBI\blast-2.7.1+\bin` . In the second picture, PATH is there, edit it. ...
written 6 months ago by ashish200
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Comment: C: genomes with lower identity display closer relationship than genomes with higher
... > Shouldn't the genomes with higher similarity closer to each other Yes, this is true but you are looking at percentage identity which is different from percentage similarity. Take a look at Sebastian's answer [here][1] . He also gives an example similar to your problem. [1]: https://www.res ...
written 8 months ago by ashish200
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Comment: C: BLAST Command Line - restarting
... You need to go to the system settings, add the blast/bin folder to the path variable after which blast can be used from cmd without typing the full address. I don't know of any way to set path variable in R. However, [this][1] might be of some help to you. [1]: https://stackoverflow.com/question ...
written 8 months ago by ashish200
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Answer: C: BLAST Command Line - restarting
... You need to put the blast/bin folder location in your path variable. see [this][1] for instructions. [1]: https://www.java.com/en/download/help/path.xml ...
written 9 months ago by ashish200
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Comment: C: What's fascinating about Bioinformatics for potential students?
... I've been a biology student till MSc and now entering bioinformatics, so maybe I can shed some light on the topic. I completed MSc in molecular biology last year. Afterwards I joined a project which was pure wet lab where after doing several PCRs, qPCRs, blots etc. for almost 6 months (not to menti ...
written 10 months ago by ashish200
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Comment: C: Eukaryotic Genome Annotation - Without ESTs or Transcriptomic or Proteomic Data
... What is your species name? Did you try Augustus. It can perform *ab initio* predictions but it requires a species name. See the list at the end of [this page][1] You can try using the best annotated species of the phylum in which your species of interest belongs. [1]: http://bioinf.uni-greifswald ...
written 10 months ago by ashish200
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Comment: C: bowtie2-align exited with value 139
... Use `top` to see all the running processes, see which process is using maximum memory, kill it or wait for it to finish and then run bowtie2. I work on plants and use different tools. To run your job on my system I'll have to setup many things. ...
written 10 months ago by ashish200
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Comment: C: bowtie2-align exited with value 139
... The error (segmentation fault) is a memory issue. It means you are trying to access memory you don't have access to. However, bowtie2 works fine on a laptop with only 4Gb RAM. I've seen that if the free memory is less than 50gb, jobs do not run. Maybe the cluster itself requires more than 20gb to wo ...
written 10 months ago by ashish200
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Answer: C: Question about Gene ID with different Transcription ID
... Do not add FPKM values from each transcripts, leave them as they are. Look at individual transcripts and their annotations, many genes code for different transcripts which will have different functions. Also, you will do real time PCR on transcripts not on the gene, so stick to the transcripts. Whe ...
written 10 months ago by ashish200

Latest awards to ashish

Popular Question 11 weeks ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 4 months ago, created a question with more than 1,000 views. For retrieving best hit in local blast output
Popular Question 6 months ago, created a question with more than 1,000 views. For how to analyse gene expression using RNA-seq data
Popular Question 7 months ago, created a question with more than 1,000 views. For how to analyse gene expression using RNA-seq data
Popular Question 9 months ago, created a question with more than 1,000 views. For heatmap using FPKM values
Supporter 13 months ago, voted at least 25 times.
Scholar 20 months ago, created an answer that has been accepted. For A: please help me retrieve these sequences

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