Tailer: A tool for 3' end analysis of non-polyadenylated RNAs from 3' sequencing data
Requirements
Python >= 3.6pysamBiogffuitlsrequeststqdm
Installation
pip install jla-tailer
Usage
Global alignment with a GTF annotation and SAM/BAM formatted files
Tailer -a [GTF Annotation] [SAM or BAM Files]
Required Arguments
-a, --annotation- GTF formatted database to be used to infer 3' ends. Ensembl GTFs have worked well for this pipeline
[SAM or BAM Files]- Space separated list of sam/bam formatted file locations to perform 3' end tail analysis
Local alignment with with FASTA/Q and specific Ensembl IDs of interest or reference fasta
Tailer -e [comma separated list of EnsIDs no spaces] [FASTA/Q files]
Tailer -f fasta_reference_file.fasta [FASTA/Q files]
Required Arguments
-e, --ensids- Comma separated list of ensembl IDs. Either -e or -f inputs are required.
-f, --fasta- FASTA formatted file to align reads against. Either -f or -e inputs are required
[Trimmed FASTQ files]- Space separated FASTQ file locations for analysis.
Optional arguments
-t, --threshold [int, default=100]- Any alignment identified further than this distance in nucleotides from the mature end will be considered spurious and discarded
-x, --trim [int, default=0]- Helper for local mode only, can remove X nucleotides from adapter on the 3' end
-read, --read [int, default=1]- Paired end only. 1 or 2 to signify which end contains the 3' end information.
-r, --rev_comp- If set, will reverse complement the reads. Necessary for some library prep methods
-f, --fasta- Use a fasta file as a reference instead of building one from ensembl IDs (Local Only)
-s, --sequence- Output sequence in the tail file. Useful for debugging.
miRNA tailing (in development)
Tailer --miRNA [sam files]
Determines tails using an alignment file (SAM/BAM) that was aligned to a fasta genome of mature miRNAs
Optional arguments
--rpad [int, default=0]- Number of downstream nucleotides added to distinguish between post-transcriptional and genome-encoded tails
1 maintainer
Metadata
1 maintainer
Release files for jla-tailer 0.1.18
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| jla-tailer-0.1.18.tar.gz | 12.4 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| jla_tailer-0.1.18-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 26.6 kB
Release files / jla-tailer-0.1.18.tar.gz
| Download URL | jla-tailer-0.1.18.tar.gz |
|---|---|
| Size | 12.4 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
29ef9a6dee3c37467ba67a7dca000a0723607e8c400a5429c20eaf70681f6efe
|
|
BLAKE2b-256 checksum How to use checksums |
0734c749189431cf822392c4f80fb154921c8a7fd058f23d8668d39c5b8adfee
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.4.2 importlib_metadata/3.10.0 pkginfo/1.7.0 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.62.2 CPython/3.8.8
|
Release files / jla_tailer-0.1.18-py3-none-any.whl
| Download URL | jla_tailer-0.1.18-py3-none-any.whl |
|---|---|
| Size | 14.2 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
3dd76cb1ace746469ab701e4876515940f63c4fb96332f39e8c99d363fbb59be
|
|
BLAKE2b-256 checksum How to use checksums |
5e26fabab33b60f9d0f6598d00f3aed01fde0a13f6da477bea15513701b661ae
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.4.2 importlib_metadata/3.10.0 pkginfo/1.7.0 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.62.2 CPython/3.8.8
|
Security for jla-tailer 0.1.18
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
