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Welcome to the Subread forum!

I hope you find this forum useful. Any comments and suggestions are welcome. When you report a bug, please provide as much details as possible, such as version, error messages and the commands you used. This will help us to reproduce the problems and fix them as quickly as possible.

News and major updates will be announced in this forum as well.

Wei Shi

On behalf of the Subread team

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hisoph, Yang LIAO4

4/15/21

Successfully assigned fragments is low

Glad to hear that the assigned rate is higher. 57% isn't a very low rate especially when you'

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Successfully assigned fragments is low

Glad to hear that the assigned rate is higher. 57% isn't a very low rate especially when you'

4/15/21

1/3/21

Is SAF format 0 based or 1 based?

The coordinates in the SAF format are 1-based coordinates. On Monday, 4 January 2021 at 1:54:44 pm

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Is SAF format 0 based or 1 based?

The coordinates in the SAF format are 1-based coordinates. On Monday, 4 January 2021 at 1:54:44 pm

1/3/21

11/2/20

Is sorting by read name processed in the case of single reads with multiple mappings?

Hi Yang, I'm wondering how sorting works on single reads with multi-mapping: is sorting by read

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Is sorting by read name processed in the case of single reads with multiple mappings?

Hi Yang, I'm wondering how sorting works on single reads with multi-mapping: is sorting by read

11/2/20

martina, Yang LIAO2

10/30/20

Which FC function is handling the automatic PE name sorting?

Hi Martina, FeatureCounts matches read pairs by read names, then the "mate mapping locations

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Which FC function is handling the automatic PE name sorting?

Hi Martina, FeatureCounts matches read pairs by read names, then the "mate mapping locations

10/30/20

Мария Романова, … Wei Shi4

10/30/20

Junction counting and filter out low mapping quality reads

I understand. Thank you very much for your response. пятница, 30 октября 2020 г. в 01:42:35 UTC+3,

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Junction counting and filter out low mapping quality reads

I understand. Thank you very much for your response. пятница, 30 октября 2020 г. в 01:42:35 UTC+3,

10/30/20

martina, Yang LIAO2

10/29/20

Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?

Hi Martina, FeatureCounts doesn't use the read sequences (SEQ) and quality strings (QUAL) in the

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Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?

Hi Martina, FeatureCounts doesn't use the read sequences (SEQ) and quality strings (QUAL) in the

10/29/20

James D. Lauderdale, Yang LIAO2

10/20/20

No successful assigned alignments using featureCounts

Hi James, I took a look at the GTF file and BAM file, and they used very different sequence names.

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No successful assigned alignments using featureCounts

Hi James, I took a look at the GTF file and BAM file, and they used very different sequence names.

10/20/20

Chi Sutherland, Yang LIAO2

10/20/20

featureCounts overlap settings

Hi Chi, The "--minOverlap" option works on both reads and features, namely it gives the

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featureCounts overlap settings

Hi Chi, The "--minOverlap" option works on both reads and features, namely it gives the

10/20/20

wang...@gmail.com, Yang LIAO3

9/27/20

How does featurecounts deal with the output from Bowtie?

Hi Yang, Thanks for the answer. I have some further questions regarding this. It has been reported

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How does featurecounts deal with the output from Bowtie?

Hi Yang, Thanks for the answer. I have some further questions regarding this. It has been reported

9/27/20

kistina...@gmail.com, … Wei Shi11

9/23/20

featureCounts output

You can set GTF.attrType = "db_xref" in your featureCounts command to get Entrez gene IDs,

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featureCounts output

You can set GTF.attrType = "db_xref" in your featureCounts command to get Entrez gene IDs,

9/23/20

Shun Liu, Yang LIAO2

7/7/20

Does featureCounts keep or filter specific length of reads?

You can specify the minimum overlap length between a read and a feature (or meta-feature). This can

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Does featureCounts keep or filter specific length of reads?

You can specify the minimum overlap length between a read and a feature (or meta-feature). This can

7/7/20

Pedro Silva, Yang LIAO2

6/15/20

"ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file."

As suggested in the screen output, the GTF annotation from NCBI RefSeq contains empty gene_id values.

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"ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file."

As suggested in the screen output, the GTF annotation from NCBI RefSeq contains empty gene_id values.

6/15/20

Marie Strader, Yang LIAO2

6/14/20

gene counts with gff3

The chromosome names in your GTF file is like chr10, but the chromosome names in your BAM file are

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gene counts with gff3

The chromosome names in your GTF file is like chr10, but the chromosome names in your BAM file are

6/14/20

J Summe, Yang LIAO8

6/14/20

R session aborts with featureCounts

Thanks, Summe. I have had your GTF file. This GTF file has many lines that don't follow the GTF

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R session aborts with featureCounts

Thanks, Summe. I have had your GTF file. This GTF file has many lines that don't follow the GTF

6/14/20

Ina Hoeschele, Yang LIAO2

6/10/20

SAF format error

You should remove the quotation marks in the SAF file -- the columns are delimited by TAB characters

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SAF format error

You should remove the quotation marks in the SAF file -- the columns are delimited by TAB characters

6/10/20

Payton Yau, Wei Shi2

5/18/20

RNA-Seq data from FFPE samples

Dear Payton, I dont have much experience with FFPE samples but you should take caution if you would

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RNA-Seq data from FFPE samples

Dear Payton, I dont have much experience with FFPE samples but you should take caution if you would

5/18/20

R adele, Yang LIAO7

4/29/20

Featurecounts exon output

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Featurecounts exon output

4/29/20

R adele, Wei Shi3

4/29/20

Retrieving RPKM, FPKM, AND TPM values

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Retrieving RPKM, FPKM, AND TPM values

4/29/20

Kamil Slowikowski, … Marcelo Laia8

4/21/20

Please describe the featureCounts summary

Dear All! I found this figure (https://www.mathworks.com/help/bioinfo/ref/featurecount_overlapmethod.

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Please describe the featureCounts summary

Dear All! I found this figure (https://www.mathworks.com/help/bioinfo/ref/featurecount_overlapmethod.

4/21/20

Edward Wallace, Wei Shi2

4/16/20

featureCounts for multiple features

Dear Edward, Apologies for my delayed response. I have been busy with moving my lab to a different

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featureCounts for multiple features

Dear Edward, Apologies for my delayed response. I have been busy with moving my lab to a different

4/16/20

Setshaba Taukobong, Yang LIAO2

4/15/20

Your annotation file contains many long lines. There was a bug making Rsubread unable to parse the

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Your annotation file contains many long lines. There was a bug making Rsubread unable to parse the

4/15/20

Gert Hulselmans, … Wei Shi12

4/6/20

Support counting reads per cell barcode in featureCounts

CellCounts currently does not support the counting of mapping results from a third-party aligner, but

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Support counting reads per cell barcode in featureCounts

CellCounts currently does not support the counting of mapping results from a third-party aligner, but

4/6/20

Peter Hoyt, Yang LIAO3

3/17/20

buildindex: Working for some genomes others give "-1" in .files file

Thanks very much for your reply and for checking whether this affects my downstream analyses. I very

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buildindex: Working for some genomes others give "-1" in .files file

Thanks very much for your reply and for checking whether this affects my downstream analyses. I very

3/17/20

Ilya Mazo, Yang LIAO2

2/24/20

The GFF and GFF3 formats are supported by featureCounts .

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The GFF and GFF3 formats are supported by featureCounts .

2/24/20

Philip Lijnzaad, Yang LIAO9

1/30/20

core dumps (failed assertion?) in SAM_pairer_update_orphant_table

Thanks for sharing the data! I'm not sure if the pure "N" read sequences in foo . bam

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core dumps (failed assertion?) in SAM_pairer_update_orphant_table

Thanks for sharing the data! I'm not sure if the pure "N" read sequences in foo . bam

1/30/20

Dapeng Wang, Yang LIAO2

1/28/20

featurecounts output changes the underscores in the sample name into dots

I agree that the underscores should be kept unchanged in the returned object from featureCounts . We

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featurecounts output changes the underscores in the sample name into dots

I agree that the underscores should be kept unchanged in the returned object from featureCounts . We

1/28/20

R adele, Wei Shi8

1/7/20

Turning on '--donotsort' option could lead to incorrect counting results if your BAM/SAM

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Turning on '--donotsort' option could lead to incorrect counting results if your BAM/SAM

1/7/20

R adele, Yang LIAO2

12/19/19

read counting at the exon level

Using "gencode.v19.annotation.gtf" (I assume that it is the "Comprehensive gene

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read counting at the exon level

Using "gencode.v19.annotation.gtf" (I assume that it is the "Comprehensive gene

12/19/19

R adele, Yang LIAO3

12/19/19

using −−donotsort command with Featurecounts

Thanks Yang Liao for answering my question

unread,

using −−donotsort command with Featurecounts

Thanks Yang Liao for answering my question

12/19/19

Pham Luong Thang, Yang LIAO3

12/18/19

Install Subread 2.0 for Ubuntu 18.04

Thank you so much for your help.

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Install Subread 2.0 for Ubuntu 18.04

Thank you so much for your help.

12/18/19

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