User: chahatupretiiitk

Reputation:
20
Status:
New User
Location:
United States
Last seen:
19 hours ago
Joined:
2 years, 8 months ago
Email:
c***************@gmail.com

Posts by chahatupretiiitk

<prev • 15 results • page 1 of 2 • next >
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Finding RNA sequences for a list of genes
... I have the data from an RNA-seq experiment, and as a result I have a list of genes with their corresponding number of genes. I have been able to do some filtering and as a result, I have finally a list of 200 genes. For this list, I want to run MEME so as to see if there is anything common motif in ...
list genes rna rna-seq written 1 day ago by chahatupretiiitk20
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Comment: C: Where to find a list of rat protein coding genes?
... Thank you so much, Biomart is awesome! And so is Biostars! ...
written 7 days ago by chahatupretiiitk20
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Where to find a list of rat protein coding genes?
... I have a list of rat genes and I wanted to filter out the protein coding genes from that (It also has antisense RNA, lnc RNA, snRNA... etc.). So for that I needed a list of all protein coding genes in rat. Where can I get this list? I do know that for human and mouse, it can be obtained from GenC ...
genome rat gene-list written 7 days ago by chahatupretiiitk20
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Do I need to merge bai files also, while merging bam files
... I have 10 folders, each containing a bam file and a corresponding bai file. I need to merge the bam files, which I believe I can do with `samtools merge merged_filename.bam *.bam`. My question is that do I need to also merge the corresponding bai files as well? And if so, should I just do - `samto ...
bam rna-seq written 8 days ago by chahatupretiiitk20 • updated 8 days ago by Gabriel R.2.1k
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Comment: C: Error in creating a volcano plot in MATLAB
... Thanks Devon for letting me know that this is not recommended. Will take care of it from now on ...
written 21 days ago by chahatupretiiitk20
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Error in creating a volcano plot in MATLAB
... I am a complete newbie to MATLAB and the first task I have is to create a volcano plot. I have been using this link to understand about it and get started - https://www.mathworks.com/help/bioinfo/ref/mavolcanoplot.html I tried to run it on dummy values - a=[1 2 3] b=[4.6 2.7 4.5] c=[0.05 0.33 0 ...
matlab rna-seq plot written 21 days ago by chahatupretiiitk20
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Comment: C: SRAtoolkit: error while running sam-dump
... hi, thanks for your comment. Yes, I do have a pre-downloaded SRA file and the error is as shown. Thank you for the link for the SRA file (I had downloaded it from the corresponding GEO file). How do you suggest I should align the data myself? I am a complete beginner in this. ...
written 4 weeks ago by chahatupretiiitk20
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Comment: C: SRAtoolkit: error while running sam-dump
... Hi, is the command I wrote supposed to involve some kind of download? I thought the command was just supposed to convert a SRA file to SAM format. Also, looking at the error I pasted here, do you have any idea what the problem could be? ...
written 4 weeks ago by chahatupretiiitk20
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SRAtoolkit: error while running sam-dump
... Hi, I am trying to convert an SRA file to the SAM format, and I am using the following command (Ubuntu 17.04) - sam-dump --output-file out.sam SRR3031662 But after a while of running, it gave the following error - 2017-09-19T23:21:57 sam-dump.2.8.1 sys: libs/kns/unix/syssock.c:524:KSock ...
ncbi sra sam sratoolkit written 4 weeks ago by chahatupretiiitk20
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Comment: C: Is it possible to search Pubmed articles for a specific organism?
... Thanks Pierre for the answer. I checked out the answer you have linked but the corresponding URL does not give any article results, just some XML text, and not the ID/link of the paper you mention right after it. Also, since I am new to NCBI e-utils, I didn't understand how to > first search fo ...
written 5 months ago by chahatupretiiitk20

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