User: dbpzdbpz

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dbpzdbpz140
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Posts by dbpzdbpz

<prev • 11 results • page 1 of 2 • next >
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Answer: A: featureCounts log: "WARNING contig is not found in the provided genome file!"
... I downloaded HanXRQr1.0-20151230.fa (I assume that it is the scaffold file on www.heliagene.org). Indeed, it has spaces in the contig names like >HaXRQ-20151104-s00077 len=1683791 FeatureCounts treated the whole string, including "len=....", as the contig name, hence it cannot match the co ...
written 6 months ago by dbpzdbpz140
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Comment: C: featureCounts log: "WARNING contig is not found in the provided genome file!"
... The WARNING message indicates that featureCounts didn't find the HanXRQCP sequence in the fasta file but it is mentioned in the BAM file. Can you try this: cat /path/to/file/HanXRQr1.0-20151230.fa | grep HanXRQCP Maybe the format is a little tricky so featureCounts misinterpreted the sequence ...
written 6 months ago by dbpzdbpz140
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Answer: A: FeatureCounts summarizing at exon level
... The "-B" option is not necessary for exon-level counting, but it can improve (maybe very little) the accuracy of analysis by not considering the read-pairs that are suspiciously low-quality. The "-O" option is not necessary if your aligner is not junction-aware, namely they don't report the exon-ex ...
written 2.1 years ago by dbpzdbpz140
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Answer: A: Creating SAF data table for featureCounts for viral RNA-Seq
... The "Chr" values in the annotations for featureCounts don't need to be chromosome names. They can be contig names or anything as long as the names coincide with the chromosome names in your SAM or BAM files (in the @SQ header lines and also the third column of the alignment results). In your case, ...
written 2.2 years ago by dbpzdbpz140
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Answer: A: featureCounts duplicate counting
... When you specified "--ignoreDup", featureCounts will test the FLAGS field in the SAM/BAM file to see if it is a duplicated mapping. In particular, the bit in the FLAGS being tested is 0x400 (1024). This bit is set by the aligner according to its own strategy. Based on the summarization information ...
written 6.0 years ago by dbpzdbpz140
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Answer: A: Intron level featureCounts gives segfault
... Sorry for the segmentation faults. There were two bugs in the old version of featureCounts in R that were related to the annotation files and were able to crash the R session. These two bugs have been fixed in the new Rsubread package. The new package is available on BioC 2.14. The version of the n ...
written 6.2 years ago by dbpzdbpz140
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Comment: C: how to use a bed file with htseq-count
... Sorry that there were two annotation-related bugs in the old featureCounts-1.4.4 version that can crash the program. We have fixed the bugs and made a new release (1.4.5) yesterday: http://sourceforge.net/projects/subread/files/subread-1.4.5/ Can you please try the new version? I hope it can finis ...
written 6.2 years ago by dbpzdbpz140 • updated 10 months ago by RamRS28k
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Comment: C: Remove duplicates in featurecounts
... Sorry that it was delayed for weeks. The 1.4.5 version of subread (inc. featureCounts) was released yesterday on sf.net. http://sourceforge.net/projects/subread/ ...
written 6.2 years ago by dbpzdbpz140 • updated 10 months ago by RamRS28k
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Answer: A: Remove duplicates in featurecounts
... The new version of subread (1.4.5) will provide a function to ignore reads or fragments that have the 0x400 flag (the duplicate read flag). This version should be released in days. ...
written 6.2 years ago by dbpzdbpz140
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Answer: A: Compariosn Htseq And Feature Count
... I think it is interesting to compare the two programs. FeatureCounts runs much faster and supports more input formats (including BAM files that are sorted by either read names or genomic coordinates). But it is also important to compare the read assignment results after all. For single-end reads, t ...
written 6.4 years ago by dbpzdbpz140 • updated 10 months ago by RamRS28k

Latest awards to dbpzdbpz

Scholar 2.2 years ago, created an answer that has been accepted. For A: featureCounts duplicate counting
Scholar 6.0 years ago, created an answer that has been accepted. For A: featureCounts duplicate counting

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