Moderator: Goutham Atla
Goutham Atla ♦ 7.2k
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Computational Biology. Marie-Curie ESR. Regulatory genomics. Beta-cell biology.
Posts by Goutham Atla
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... you can post the reason. might be helpful for others. ...
written 18 days ago by
Goutham Atla ♦ 7.2k
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... As far as I know, if you have the PacBio full-length cDNA , you already have the transcripts. Most of the PacBio analysis tools generates a GTF file at the end. I would generate the gene models from the transcript models and quantify the genes using illumina reads to get the expression levels of gen ...
written 18 days ago by
Goutham Atla ♦ 7.2k
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... Workaround: Index the bam file using samtools, and make sure both bam and index are in same folder. Most of the tools tries to index bam only if there is no index available.
Regarding the error, give more details about the error. There could be several reasons why a bam file can not be indexed. ...
written 18 days ago by
Goutham Atla ♦ 7.2k
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... Did you do PCA analysis on your replicate samples ? ...
written 4 weeks ago by
Goutham Atla ♦ 7.2k
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... As Devon suggested, I always consider R1 and ignore R2 if a sample is paired-end and rest of the samples are single-ended. This should not be a major problem in calling peaks or quantifying the peaks as far as I know. ...
written 6 weeks ago by
Goutham Atla ♦ 7.2k
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Comment:
C: using DREME and .broadpeak file
... What kind of Chip-Seq data it is ? ...
written 8 weeks ago by
Goutham Atla ♦ 7.2k
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... feautureCounts should do the trick. It has an R interface or command line version. You need to convert your peak coordinates to SAF format as given on their website. ...
written 9 weeks ago by
Goutham Atla ♦ 7.2k
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Comment:
C: Picard vs samtools rmdup
... post exact commands and `samtools flagstat` output before and after removing duplicates ...
written 12 weeks ago by
Goutham Atla ♦ 7.2k
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... Its need not be scaling treatment to control always. It scales the sample with large number of reads to sample with smaller number of reads. ...
written 12 weeks ago by
Goutham Atla ♦ 7.2k
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... I would pool all control samples and call peaks on each treatment sample independently.
macs2 callpeak -t tfile1.bam -c ctrl_pooled.bam ...
written 12 weeks ago by
Goutham Atla ♦ 7.2k
Latest awards to Goutham Atla
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16 days ago,
created a question with more than 10,000 views.
For Understanding Samtools Flagstat Output
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For Google genomics cloud platform ?
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For A: Breaking down the reference genome chromosome-wise
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For A: htseq-count for RNA Seq
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For Annotation Bed File For Phaseolus Vulgaris
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For A: Breaking down the reference genome chromosome-wise
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For Confusion In Pdb File Format
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For A: Breaking down the reference genome chromosome-wise
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For C: bioinformatics basic training
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For Confusion In Pdb File Format
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6 months ago,
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For A: Breaking down the reference genome chromosome-wise
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6 months ago,
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For Confusion In Pdb File Format
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6 months ago,
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For A: Breaking down the reference genome chromosome-wise
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For A: What are the biggest challenges bioinformaticians have with data analysis?
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For C: bioinformatics basic training
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For A: Breaking down the reference genome chromosome-wise
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