[marcora]

Hi Manoj,

I don't provide binary packages for MacOS -- it's too complicated as I don't have a Mac myself. Please install XCode and use it. (Actually, you only need GCC, but installing all of XCode is easiest.)

XCode comes with MacOS and can be found on the second of the two MacOS installation CDs. So, there is no need to download it.

(If a Mac user reading this wants to help out Manoj: Run the command 'python setup.py bdist' in the unpacked tarball, and a binary package will be built automatically and packed into a single file.)

Simon

Here we go!

[Simon Anders]

Hi Manoj,

I don't provide binary packages for MacOS -- it's too complicated as I don't have a Mac myself. Please install XCode and use it. (Actually, you only need GCC, but installing all of XCode is easiest.)

XCode comes with MacOS and can be found on the second of the two MacOS installation CDs. So, there is no need to download it.

(If a Mac user reading this wants to help out Manoj: Run the command 'python setup.py bdist' in the unpacked tarball, and a binary package will be built automatically and packed into a single file.)

Simon

[mmpillai]

Hi Simon,
I heed your advice re: the OS - I have succesfully installed HTSeq in my linux system. I wanted to install it from binary on my Mac, but the binary package is not available for download on PyPI. (I dont want to download XCode - seems like it is >3.5 Gb in size ).
Thanks again, bioinformatics clearly being the bottleneck for high throughput applications, packages such as yours is clearly very helpful.
Manoj

[naluru]

htseq-count for miRNA

I am using "htseq-count" to count the miRNA using their genomic coordinates. It worked very well. But, I am also interested in a more detailed output. I want an output with each and every aligned read and their counts. The reason for this is, there are lot of miRNA length variants, mature star and precursor sequences. It would be nice to see the proportion of different reads. Right now, I can only see the counts of all precursor miRNAs.

I would like to know if there is any way to get that information and can provide some hints that will be highly appreciated.

Thank you in advance.

[marcora]

Hi Keith
At the moment, HTSeq can natively only work with SAM files. Adding BAM support is on my to-do list, and of course, I would do it by simply wrapping the samtools.

Cheers
Simon

Hi Simon,

is BAM support in HTSeq coming soon!?!

Keep up the good work!

[alvin]

Hi Alvaro



As you are by now the fourth person requesting this feature, I thought I'd no longer only make promises to add it in the future but rather get it done. :-)

The new version, 0.4.7, now offers a new option, "-o", for htseq-count. If you add '-o', followed by a filename, a SAM file of this name will be written that contains the same lines as the input SAM file, but with each line appended by an optional field, with tag 'XF', that indicates how the read was counted, i.e., it is either a gene name, or a special counter name like "no_feature". With grep and cut, you can then get what you want.

Simon

Great! I found the -o option very useful.
Thank you very much for your help.
Best Regards


Álvaro Pena

[Simon Anders]

Hi Alvaro

I wonder if it possible to retrieve the id of the reads that has "no feature" in htseq-count.
I'm interested in those reads that do not overlap with any annotated gene.
I would really appreciate any suggestion.

As you are by now the fourth person requesting this feature, I thought I'd no longer only make promises to add it in the future but rather get it done. :-)

The new version, 0.4.7, now offers a new option, "-o", for htseq-count. If you add '-o', followed by a filename, a SAM file of this name will be written that contains the same lines as the input SAM file, but with each line appended by an optional field, with tag 'XF', that indicates how the read was counted, i.e., it is either a gene name, or a special counter name like "no_feature". With grep and cut, you can then get what you want.

Simon

[Simon Anders]

Hi

Hi,
I am trying to install 04.5p5 on windows. I get this error when I run the setup.py on a shell
Traceback (most recent call last):
File "C:\Python26\Lib\site-packages\HTSeq-0.4.5p5\setup.py", line 62, in <module>
'scripts/htseq-count',
File "C:\Python26\lib\distutils\core.py", line 140, in setup
raise SystemExit, gen_usage(dist.script_name) + "\nerror: %s" % msg
SystemExit: usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: setup.py --help [cmd1 cmd2 ...]
or: setup.py --help-commands
or: setup.py cmd --help

error: no commands supplied
Please help, all help is very much appreciated.
Thanks
Manoj

Please read the installation instructions:

http://www-huber.embl.de/users/anders/HTSeq/doc/install.html

I haven't made a Windows binary package for a while, though.

(I still have trouble understanding why anybody would want to do HTS bioinformatics on Windows. Nearly all bioinformatics developers work on GNU systems (Linux or Mac OS). Ensuring that a tool developed on Linux works on a Mac, or vice versa, is trivial, but supporting Windows is always extra work, and hence has low priority for us developers, which makes Windows a bad choice for users, too.)

Simon

[alvin]

No Feature

Hi!
I wonder if it possible to retrieve the id of the reads that has "no feature" in htseq-count.
I'm interested in those reads that do not overlap with any annotated gene.
I would really appreciate any suggestion.
Thanks
Best regards.


Alvaro Pena

[mmpillai]

Hi,
I am trying to install 04.5p5 on windows. I get this error when I run the setup.py on a shell
Traceback (most recent call last):
File "C:\Python26\Lib\site-packages\HTSeq-0.4.5p5\setup.py", line 62, in <module>
'scripts/htseq-count',
File "C:\Python26\lib\distutils\core.py", line 140, in setup
raise SystemExit, gen_usage(dist.script_name) + "\nerror: %s" % msg
SystemExit: usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: setup.py --help [cmd1 cmd2 ...]
or: setup.py --help-commands
or: setup.py cmd --help

error: no commands supplied
Please help, all help is very much appreciated.
Thanks
Manoj

[agali]

Hi Simon,

The SAM file is from SHRiMP. I looked up the file format specification and I think there should be a '*' in the QUAL field when there is a '*' in the SEQ field..
I will try to put an extra column in my SAM file and then run it on HTSeq.

Thanks!
Aga

[Simon Anders]

Hi

2_512_865_F3 16 Esi0595_0002 conserved unknown protein [1335] f:2354-3688 613 255 3H47M * 0 0 * AS:i:347

Your SAM file is incorrect. According to the specs, a SAM file has the following fields:

<QNAME> <FLAG> <RNAME> <POS> <MAPQ> <CIGAR> <MRNM> <MPOS> <ISIZE> <SEQ> <QUAL> [<TAG>:<VTYPE>:<VALUE> [...]]

I try to align your fields to the field names:

QNAME: 2_512_865_F3
FLAG: 16
RNAME: Esi0595_0002 conserved unknown protein [1335] f:2354-3688 (assuming these are all spaces and no tags in here)
POS: 613
MAPQ: 255
CIGAR: 3H47M
MRNM: *
MPOS: 0
ISIZE: 0
SEQ: *
QUAL: AS:i:347
TAG:VTYPE:VALUE:

Obviously, "AS:i:347" is a tag and should hence be in the 12th column. It is, however, in the 11th column, and hence read as quality string.

Where did you get this SAM file from?

Simon

[agali]

Hi,

I have seen a post with the same issue before, but I didn't see any replay.. I am working with SOLiD data, aligned with SHRiMP to the reference mRNA library.
I am getting this error message with htseq-count:

Error occured in line 16241 of file F_mrna.sam.
Error: ("'seq' and 'qualstr' do not have the same length.", 'line 16241 of file F_mrna.sam')
[Exception type: ValueError, raised in _HTSeq.pyx:626]

The error applies to the whole SAM file (every line will give this error).
The example line from SAM file:

2_512_865_F3 16 Esi0595_0002 conserved unknown protein [1335] f:2354-3688 613 255 3H47M * 0 0 * AS:i:347

Do you have any solutions?

Thanks.

[joro]

It's running without errors now thanks. However, the sum of column 2 in the htseq-count output file doesn't equal the number of non-header lines in the SAM file. The difference is around 40,000. Do you know what is causing this difference?

Thanks for offering to look through my input files but I've resolved this now. There were reads mapping to sequences that weren't defined in the gtf. My mistake!

[joro]

Ok thanks Simon. I'll have a go at changing the counting logic if I need to at any point! I think I only need gene-level counting for now.