User: praasu

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praasu30
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New User
Location:
Prague, Czech republic
Twitter:
prasoon84
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22 hours ago
Joined:
3 years, 3 months ago
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Posts by praasu

<prev • 31 results • page 1 of 4 • next >
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Comment: C: how to extract intron coordinates (in bed) from bam
... Hi Ryan, Today, I got to know that mRNA library is stranded. In that case, how can I obtained the strand information or why could it be missing ? Prasoon ...
written 10 weeks ago by praasu30
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Comment: C: how to extract intron coordinates (in bed) from bam
... We didn't use strand-specific library prep. ...
written 10 weeks ago by praasu30
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Comment: C: how to extract intron coordinates (in bed) from bam
... Hi Ryan, The GTF file, that I obtained from the stringTie, is missing strand information. I need strand information to check the splice sites sequence (both at 5' and 3') Do you have idea, how can I deal with that ? ...
written 11 weeks ago by praasu30
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Comment: C: ChIP-Seq TSS Line Plot
... Hi, I am using ChIPseeker, I used this command to feauture. promoter <- getBioRegion(TxDb=txdb, by = c('intron'),upstream=100, downstream=100) I wanted to only take only non-overlapping coordinate for average profile. Any suggestion ? ...
written 4 months ago by praasu30
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Comment: C: convert bedgraph to bed
... I thought it was confusing, So I changed it. The input file consists of both strand information (+/-) and score (coverage value). I want to put strand (+/-) into a separate column and score into a separate column. ...
written 6 months ago by praasu30
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Comment: C: convert bedgraph to bed
... Thank you, It is just giving first 3 column. I want to information from 4th column as well. It contains score and strand. I want to them to be separate. ...
written 6 months ago by praasu30
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convert bedgraph to bed
... I am looking for program to convert bedgraph file to bed file. Thanks a lot for you any help or suggestion in advance. Bedgraph example input : track type=bedGraph name="peaks_id76673" description="peaks in group_4271" db=mm9 color="120,101,172" priority="20" maxHeightPixels="100:50:0" altCo ...
R chip-seq rna-seq written 6 months ago by praasu30
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how to extract intron coordinates (in bed) from bam
... I have aligned raw RNA-seq reads against a reference genome with STAR. I would like to extract the intronic coordinates from obtained bam files. Any suggestion? ...
rna-seq written 8 months ago by praasu30 • updated 8 months ago by Devon Ryan96k
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Comment: C: Should I merge the Paired-end RNA-seq reads for BLAT for intron identification
... RNA-seq often consists of intronic region or unspliced reads. I was following the discussing here in https://www.biostars.org/p/42890/ ...
written 8 months ago by praasu30
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Comment: C: Should I merge the Paired-end RNA-seq reads for BLAT for intron identification
... Hi Nicolas, Thanks for your reply. I am working on the genome in which possibly non-canonical (non-GT-AG) splice sites are predominant. That's why I don't want to align with STAR. I don't know about the kallisto aligner if it is suitable for my case. ...
written 8 months ago by praasu30

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Popular Question 20 months ago, created a question with more than 1,000 views. For Extracting Intron-Exon Reads from bam files

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