From ae48a3ee9f216bd771bf65fc39f7d6d039f91f46 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Mon, 14 Jan 2013 14:23:15 -0500
Subject: [PATCH] [DOCS] new docs for bamtofastq
---
docs/content/tools/bamtofastq.rst | 100 +++++++++++++++++++++++++++++-
1 file changed, 99 insertions(+), 1 deletion(-)
diff --git a/docs/content/tools/bamtofastq.rst b/docs/content/tools/bamtofastq.rst
index 16285528..3757991d 100644
--- a/docs/content/tools/bamtofastq.rst
+++ b/docs/content/tools/bamtofastq.rst
@@ -1,3 +1,101 @@
###############
*bamtofastq*
-###############
\ No newline at end of file
+###############
+``bedtools bamtofastq`` is a conversion utility for extracting FASTQ records
+from sequence alignments in BAM format.
+
+==========================================================================
+Usage and option summary
+==========================================================================
+**Usage**:
+::
+
+ bedtools bamtofastq [OPTIONS] -i <BAM> -fq <FASTQ>
+
+**(or)**:
+::
+
+ bamToFastq [OPTIONS] -i <BAM> -fq <FASTQ>
+
+
+
+.. tabularcolumns:: |p{4.5cm}|p{8.5cm}|
+
+============= ================================================================
+Option Description
+============= ================================================================
+**-fq2** FASTQ for second end. Used if BAM contains paired-end data.
+ BAM should be sorted by query name
+ (``samtools sort -n aln.bam aln.qsort``) if creating
+ paired FASTQ with this option.
+**-tags** Create FASTQ based on the mate info in the BAM R2 and Q2 tags.
+============= ================================================================
+
+
+==========================================================================
+Default behavior
+==========================================================================
+By default, each alignment in the BAM file is converted to a FASTQ record
+in the ``-fq`` file. The order of the records in the resulting FASTQ exactly
+follows the order of the records in the BAM input file.
+
+.. code-block:: bash
+
+ $ bedtools bamtofastq -i NA18152.bam -fq NA18152.fq
+
+ $ head -8 NA18152.fq
+ @NA18152-SRR007381.35051
+ GGAGACATATCATATAAGTAATGCTAGGGTGAGTGGTAGGAAGTTTTTTCATAGGAGGTGTATGAGTTGGTCGTAGCGGAATCGGGGGTATGCTGTTCGAATTCATAAGAACAGGGAGGTTAGAAGTAGGGTCTTGGTGACAAAATATGTTGTATAGAGTTCAGGGGAGAGTGCGTCATATGTTGTTCCTAGGAAGATTGTAGTGGTGAGGGTGTTTATTATAATAATGTTTGTGTATTCGGCTATGAAGAATAGGGCGAAGGGGCCTGCGGCGTATTCGATGTTGAAGCCTGAGACTAGTTCGGACTCCCCTTCGGCAAGGTCGAA
+ +
+ <<<;;<;<;;<;;;;;;;;;;;;<<<:;;;;;;;;;;;;;;;;::::::;;;;<<;;;;;;;;;;;;;;;;;;;;;;;;;;;;<<<<<;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<<;;;;;:;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<<<;;;;;;;;;;<<<<<<<<;;;;;;;;;:;;;;;;;;;;;;;;;;;;;:;;;;8;;8888;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;8966689666666299866669:899
+ @NA18152-SRR007381.637219
+ AATGCTAGGGTGAGTGGTAGGAAGTTTTTTCATAGGAGGTGTATGAGTTGGTCGTAGCGGAATCGGGGGTATGCTGTTCGAATTCATAAGAACAGGGAGGTTAGAAGTAGGGTCTTGGTGACAAAATATGTTGTATAGAGTTCAGGGGAGAGTGCGTCATATGTTGTTCCTAGGAAGATTGTAGTGGTGAGGGTGTTTATTATAATAATGTTTGTGTATTCGGCTATGAAGAATAGGGCGAAGGGGCCTGCGGCGTATTCGATGTTGAAGCCTGAGACTAGTTCGGACTCCCCTTCCGGCAAGGTCGAA
+ +
+ <<<<<<<<<<;;<;<;;;;<<;<888888899<;;;;;;<;;;;;;;;;;;;;;;;;;;;;;;;<<<<<;;;;;;;;;<;<<<<<;;;;;;;;;;;;;<<<<;;;;;;;:::;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<<<<;;;;;;;;;;;;;;;;;;;;;;;<;;;;;;;;;;;;;;;;;;;;;;<888<;<<;;;;<<<<<<;;;;;<<<<<<<<;;;;;;;;;:;;;;888888899:::;;8;;;;;;;;;;;;;;;;;;;99;;99666896666966666600;96666669966
+
+
+
+==========================================================================
+``-fq2`` Creating two FASTQ files for paired-end sequences.
+==========================================================================
+If your BAM alignments are from paired-end sequence data, one can use the
+``-fq2`` option to create two distinct FASTQ output files --- one for
+end 1 and one for end 2.
+
+.. note::
+
+ When using this option, it is required that the BAM
+ file is sorted/grouped by the read name. This keeps the resulting records
+ in the two output FASTQ files in the same order. One can sort the BAM
+ file by query name with ``samtools sort -n aln.bam aln.qsort``.
+
+
+.. code-block:: bash
+
+ $ samtools sort -n aln.bam aln.qsort
+
+ $ bedtools bamtofastq -i aln.qsort.bam \
+ -fq aln.end1.fq \
+ -fq2 aln.end2.fq
+
+ $ head -8 aln.end1.fq
+ @SRR069529.2276/1
+ CAGGGAGAAGGAGGTAGGAAAGAGAAAGGACCAGGGAGGGGCGCATACACAGGACGCTCCGTGCGGTGATAGCAGCACCACACTGTGTTCAGTCGTCTGGC
+ +
+ =;@>==###############################################################################################
+ @SRR069529.2406/1
+ GCTGGGAAAAGGATTCAGGATGTTGGTTTCTATCTTTGAGTTGCTGCTGTGCGGCTGTCCCTACACTCGCAGTACCCCTCGGACACCGTCTACTGTGGAGG
+ +
+ =5@><<:?<?
+
+ $ head -8 aln.end2.fq
+ @SRR069529.2276/2
+ AGACCCAGAGAGGGACAGGATCTGTCCCAGATCATAAAATAGGGGGAGTGCTCCGTAGAGGCGTGCGCGGTGGCACCGTGCAGTAGTACGGGTGAGCGGGG
+ +
+ #####################################################################################################
+ @SRR069529.2406/2
+ TTCCCTACCCCTGGGGTCAGGGACTACAGCCAAGGGGAGAACTTTAGCAAGTAGACGTTAGTTATTTTGATTCCAGTGGGGACGCGCGTGTAGCGAGTTGT
+ +
+ @>=AABB?AAACABBA>@?AAAA>B@@AB@AA:B@AA@??#############################################################
+
+
--
GitLab