User: chahatupretiiitk

Reputation:
40
Status:
New User
Location:
United States
Last seen:
6 days, 20 hours ago
Joined:
2 years, 10 months ago
Email:
c***************@gmail.com

Posts by chahatupretiiitk

<prev • 37 results • page 1 of 4 • next >
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Comment: C: GTF2BED does not provide meaningful output?
... Hi Alex, But as I mentioned in my question (the 2 lines I copied from the gtf), the `transcript_id ` **is** present in the gtf. Also, what could be the reason that even the example gtf file provided in the website (foo.gtf) also generates an empty bed file? ...
written 17 days ago by chahatupretiiitk40
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GTF2BED does not provide meaningful output?
... Hi guys, I have been trying to use gtf2bed to convert a gtf file to bed format, but to no avail. On running the following command - `gtf2bed < GRCh38p5_copy.gtf > foo1.bed` it gives the error - `Error: Potentially missing gene or transcript ID from GTF attributes (malformed GTF at line [1 ...
gtf bed rna-seq written 17 days ago by chahatupretiiitk40 • updated 17 days ago by Alex Reynolds22k
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Comment: C: How to get a list of all ribosomal genes in Rat?
... Thanks a lot for the help! ...
written 19 days ago by chahatupretiiitk40
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Comment: C: How to get a list of all ribosomal genes in Rat?
... I think both approaches - through gtf and using Biomart are good ideas. However I was not sure about the the link you have mentioned in this comment. As far as I can see, it corresponds to just one rRNA gene, and I was hoping to find a list of all such genes. ...
written 19 days ago by chahatupretiiitk40
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Comment: C: How to get a list of all ribosomal genes in Rat?
... I tried to search for it online, and found that Biomart is a way to download them. So there I tried for Rat genes, but I am not sure if the version is correct. The tophat was run with Rn6 version and I was unsure if the rat data in Biomart belonged to that version. Aslo, when I downloaded the list, ...
written 19 days ago by chahatupretiiitk40
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How to get a list of all ribosomal genes in Rat?
... I have High-throughput sequencing data (cDNA from ribosomal profiling) and when I ran Fastqc on it and looked at the over-represented sequences, many of them were ribosomal genes. This is bad because the experimenters did use a protocol to remove the ribosomal RNA. Now, I mapped the reads using To ...
rat gene-list rna-seq written 19 days ago by chahatupretiiitk40 • updated 19 days ago by lshepard110
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Comment: C: Finding over-represented sequences in fastq file
... I tried it, but it's output is just a list of depth vs count, like - `#Depth Count` `1 50165628` `2 7292674` `3 2951163` `4 1563013` `5 964075` `6 652937` `7 474538` `8 360501` `9 285766` `10 232038` `...` So, I don't know what exact 'sequences' are over-represented? ...
written 4 weeks ago by chahatupretiiitk40
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Comment: C: Finding over-represented sequences in fastq file
... why do you have 2 files in1 and in2 ? Are they the mapped and unmapped reads (fastq converted from the bam)? ...
written 4 weeks ago by chahatupretiiitk40
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Comment: C: Finding over-represented sequences in fastq file
... Yes, that's a good idea, but with Jellyfish, it's not easy to get the most over-represented 'sequence' (based on the minimal experience I have with it). It allows you to dump the mer_counts to a fasta file where you can see the k-mers, but they are randomly distributed across the fasta file (not sor ...
written 4 weeks ago by chahatupretiiitk40
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Comment: C: Finding over-represented sequences in fastq file
... Thanks for your comment. I tried to blast a couple of the unmapped reads in BLAST, and the top hits were uncultured prokaryote gene, and a Streptomyces gene respectively. Many others did not return a hit when doing a BLAST search in the 'highly similar sequences' category (which is the default). Wha ...
written 4 weeks ago by chahatupretiiitk40

Latest awards to chahatupretiiitk

Student 6 weeks ago, asked a question with at least 3 up-votes. For Low mapped percentage. How to know if data is junk?
Supporter 7 weeks ago, voted at least 25 times.

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