User: CY

gravatar for CY
CY40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
1 week ago
Joined:
2 years, 1 month ago
Email:
c*******@gwmail.gwu.edu

Posts by CY

<prev • 56 results • page 1 of 6 • next >
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PCT_ribosomal base and PCT_intergenic base in standard RNA-Seq
... I have been using STAR for RNA-Seq alignment. For alignment QC based on the bam file, Picard indicates a wild range of percentage of ribosomal base (10%-50%) and percentage of intergenic base (10%-50%) across samples. I am not sure if this is normal I assume the percentage of ribosomal base depe ...
qc rna-seq written 20 days ago by CY40
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Comment: C: Two confusion in bam format
... Thanks for explaining. But different aligners set MAPQ value differently. For example bwa set MAPQ 255 as quality not available while STAR set 255 as uniquely mapped. How variant caller determine MAPQ value then? ...
written 8 weeks ago by CY40
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Two confusion in bam format
... I realized that "M" CIGAR doesn't mean no mismatch. For example, 150M doesn't mean perfect match. It could contain mismatch which is specified in MD tag. In the SAM SPEC, 'M' means **alignment match (can be a sequence match or mismatch)** My confusion is: 1) If 'M' means either alignment with ...
alignment sam bam written 8 weeks ago by CY40 • updated 8 weeks ago by Devon Ryan73k
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Comment: C: Why perfectly match (150M) records are not primary alignment in SAM
... I forgot to mention that I was using STAR. I did some searching and it seems to me that MAPQ is different for different aligner. For STAR, 255 means uniquely mapped ...
written 8 weeks ago by CY40
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Comment: C: Why perfectly match (150M) records are not primary alignment in SAM
... I was using STAR. It turns out some of the columns in bam are aligner specific, right? For example MAPQ. Also, bam generated by different aligner may keep different information. For example, STAR excludes unmapped record while bwa keeps both mapped and unmapped record. ...
written 8 weeks ago by CY40
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Comment: C: Why perfectly match (150M) records are not primary alignment in SAM
... Thanks for responding. I checked again and found out that those record with mapping quality of 255 are all primary alignment. It seems to me that mapping quality is the most important determinant for this, right? I didn't pay much attention on 'nm' tap earlier. But how comes 'nm' shows mismatch whe ...
written 8 weeks ago by CY40
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Why perfectly match (150M) records are not primary alignment in SAM
... I saw lot of record with perfect alignment (150M) but marked as secondary alignment in SAM file. For example those with FLAG number 339 or 419. The following one for example: E00477:134:H2H2NCCXx:6:2203:29267:71384 419 chr1 14479 3 150M = 14705 376 GTGGAGCCGTCCCCCC ...
alignment sam bam written 8 weeks ago by CY40 • updated 8 weeks ago by h.mon9.2k
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Answer: A: A confusion regarding haplotype
... This is maybe quick and dirty solution: In case we found all three variants and encounter two possible haplotypes, we can check variant C in dbsnp. It is most likely a minor allele. If it is frequency is reasonably low, we can assume *2 is the most likely answer. What do you think? ...
written 8 weeks ago by CY40
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Comment: C: What kind of advantage does PEAR bring?
... I guess in best case the insert size should longer than the sum of paired end reads so that the insert size can server as additional information when calling structure variant (longer insertion). When the interested region (amplicon) is short and insert size can't provide additional information, m ...
written 8 weeks ago by CY40
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Comment: C: What kind of advantage does PEAR bring?
... This is useful for identifying longer insertion only because the insert size is shorter than the sum of paired reads, right? Otherwise, The paired end reads plus the known insert size would provide more information when identifying long insertion. Am I right? ...
written 8 weeks ago by CY40

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Popular Question 16 days ago, created a question with more than 1,000 views. For Call variant from RNA-Seq data using Haplotypecaller

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