User: ATPoint

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ATPoint2.6k
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Posts by ATPoint

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Comment: C: Mapping short reads (23 b) to large catalog of short (20 b) sequences
... Bowtie has an explicit option to control for mismatches (-n). You may check out the [manual][1]. [1]: http://bowtie-bio.sourceforge.net/manual.shtml ...
written 18 hours ago by ATPoint2.6k
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Comment: C: Mappability tracks for mm10 ?
... [This][1] might help you, [1]: https://www.biostars.org/p/181014/ ...
written 19 hours ago by ATPoint2.6k
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Comment: C: How to improve alignment quality of ChIP-seq for single-end
... As far as I can see from this GSE number, all the data are paired-end. E.g. the [IgG][1] you refer to is backed up at the ENA as PE, and also the [entry at the NCBI][2] indicates paired-end. How did you download the data (in SRA format I suppose), and which command did you then use for conversion to ...
written 3 days ago by ATPoint2.6k
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Comment: C: Bam to read counts for differential expression analysis
... Sorted BAMs are not necessary, FC will sort internally if you have paired-end data (still, sorting a file is as easy as `samtools sort -o sorted.bam unsorted.bam`). I edited my post in that regard. For the checking, simply use `samtools view -f 1 in.bam | head` and then check if some reads pop up. ...
written 5 days ago by ATPoint2.6k
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Comment: C: Bam to read counts for differential expression analysis
... ...as well as multithreaded and tailored to RNA-seq. Go with featureCounts. You will need a GFF/GTF file that fits your organism/the assembly you aligned to and the BAM files. ### Assign reads to exons based on the GTF annotation: # --a = the GTF/GFF file # --F = specify the format of ...
written 5 days ago by ATPoint2.6k
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Answer: A: samtools view -bT hg19.fa OR -bhs -q 30 -F1548 A.sam > A.bam, which one is bett
... Both commands produce a proper bam file. The first command uses all entries in the sam. The second one filters out ([-F 1548][1]) unmapped reads and mates as well as reads that failed the quality control of the sequencer and marked duplicates. Also, -q 30 only takes reads qith a mapping quality abov ...
written 5 days ago by ATPoint2.6k
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Comment: C: Biological significance of Fold_enrichment in macs2
... In order to motivate people to answer, provide details on what you are working on, what you have done so far and what your view on the matter is, as Devon already suggested. ...
written 6 days ago by ATPoint2.6k
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Comment: C: samtools rmdup error
... Cool, thanks for mentioning that tool. Will check it out. I always found it a pain that Picard MarkDuplicates and SamBamba markdup are not pipe-able, especially for cohorts of WGS. ...
written 7 days ago by ATPoint2.6k
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Comment: C: samtools rmdup error
... It is perfectly fine to use rmdup, especially on larger datasets where time and IO are a limiting factor. Rmdup is not perfect, but the ultimate differences, at least in WGS, to MarkDuplikates from Picard are small, [source here][1]. [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4965708/ ...
written 7 days ago by ATPoint2.6k
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Comment: C: How do I make a schema with all described variants within a gene?
... Well, 99.9% sure that this figure was made in powerpoint. ...
written 11 days ago by ATPoint2.6k

Latest awards to ATPoint

Commentator 4 days ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
Commentator 15 days ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Commentator 20 days ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
Popular Question 22 days ago, created a question with more than 1,000 views. For Deeptools: computeMatrix - Traceback
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Teacher 26 days ago, created an answer with at least 3 up-votes. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Scholar 5 weeks ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: Bioinformatics independent research group
Scholar 5 weeks ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Scholar 5 weeks ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
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Scholar 6 weeks ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
Scholar 7 weeks ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Scholar 7 weeks ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Scholar 7 weeks ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines

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